Probes for detection of human parvovirus nucleic acid

ABSTRACT

Nucleic acid oligomers specific for human parvovirus genomic DNA are disclosed. An assay for amplifying and detecting human parvovirus genotypes 1, 2 and 3 nucleic acid in biological specimens is disclosed. Compositions for amplifying and detecting the presence of human parvovirus genotypes 1, 2 and 3 genomic DNA in human biological specimens are disclosed.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a continuation of U.S. patent application Ser. No.16/013,502, filed on Jun. 20, 2018, now allowed, which is a division ofU.S. patent application Ser. No. 14/569,338, filed on Dec. 12, 2014, nowissued as U.S. Pat. No. 10,087,494, which is a continuation of U.S.patent application Ser. No. 13/203,715, filed on Aug. 26, 2011, nowissued as U.S. Pat. No. 8,921,039, which is a national phase entry under35 U.S.C. § 371 of International Application No. PCT/US2010/025499,filed on Feb. 26, 2010, which claims the benefit of priority to U.S.Provisional Application No. 61/155,685, filed on Feb. 26, 2009, each ofwhich is incorporated herein by reference in its entirety.

REFERENCE TO SEQUENCE LISTING

The instant application contains a Sequence Listing which has beensubmitted in ASCII format via EFS-Web and is hereby incorporated byreference in its entirety. Said ASCII Copy, created on Jan. 6, 2021, isnamed “Seq_Listinggp234-pct_ST25” and is 38,019 bytes in size.

FIELD OF THE INVENTION

This invention relates to diagnostic methods and compositions fordetecting a human infectious agent, and specifically relates to methodsand compositions for detecting in vitro the nucleic acid of humanparvovirus genotypes 1, 2 and 3.

BACKGROUND OF THE INVENTION

Human parvovirus (genus Erythrovirus) is a blood borne, non-envelopedvirus that has a single-stranded DNA (ssDNA) genome of about 5.5 kb(Shade et al., 1986, J. Virol. 58(3): 921-936, Brown et al., 1997, Ann.Rev. Med. 48: 59-67). Individual virions contain one copy of either theplus or minus strand of the genome, represented in approximately equalnumbers. The ssDNA genome has inverted terminal repeats that form 5′ and3′ hairpins of about 350 nt, which are essential for viral replication.The genome includes two open reading frames on the plus strand, whichcode for structural proteins (VP1 and VP2) and non-structural protein(NS1).

At one time it was believed that human parvovirus was highly conservedat less than 2% genetic diversity. More recently, though, it has beendiscovered that a human Erythrovirus isolate, originally termed V9, hasa greater than 11% divergence in genome sequence compared to B19, withthe most striking DNA dissimilarity is >20%, observed within the p6promoter region. The V9 isolate was determined to have a clinicalpresence of greater than 11%, as well. Now the human Erythrovirus groupis divided into three distinct virus genotypes: genotype 1 (B19),genotype 2 (A6- and LaLi-like), and genotype 3 (V9-like). (Servant etal., 2002, J. Virol. 76(18): 9124-34; Ekman et al., 2007, J. Virol.81(13): 6927-35). Servant et al., refer to genotype 1 as virusescorresponding to parvovirus B19 and refer to genotypes 2 and 3 asviruses corresponding to parvovirus V9-related. Ekman et al., refer togenotypes 1-3 as all corresponding to parvovirus B19. For convenienceherein, genotypes 1, 2 and 3 are referred to as parvovirus genotypes 1,2 and 3 or human parvovirus genotypes 1, 2 and 3.

Current nucleic acid detection assays do not accurately detect allparvovirus genotypes. As a result of these deficient assays, many plasmapools remain contaminated with human parvovirus. Similarly, many casesof parvovirus infection are not properly diagnosed. Thus, there is aneed for a nucleic acid test that detects human parvovirus genotypes 1,2 and 3.

Infection with human parvovirus can occur via respiratory transmissionor through infected blood or blood products. Viremia reaches high levelsat about a week after inoculation, and is generally cleared within abouttwo weeks following infection. Infected individuals may exhibit nosymptoms, or have erythema infectiosum symptoms that include mildflu-like symptoms, rash, and/or temporary arthritis-like joint pain(arthropathy). Children are more likely than adults to develop the rash(called “fifth disease”), whereas arthropathy is a common symptom inadults. More serious problems occur in susceptible patients, includingaplastic crisis in patients with hemolytic anemias, and persistentparvovirus infection and other hematologic changes in immunosuppressedpatients. In women, human parvovirus infections have been associatedwith loss of about 10% of early pregnancies due to fetal death. Thus,the failure to detect parvovirus in a pooled plasma sample or fordiagnosis of infection has serious consequences.

Parvovirus is a relatively resistant to viral inactivation, e.g., bychemical or heat-treatment methods used to destroy infective particlesin blood, serum or plasma. Also, high viral concentrations in a samplemay overwhelm viral depletion methods used to remove viral contaminantsfrom the sample. Parvovirus in blood, plasma or plasma-derived productscan infect additional individuals who receive contaminated transfusionsor products. Plasma derivatives are often made from pooled donations(e.g., a pool of thousands of individual donations) resulting in therisk that a single contaminated donation could contaminate the pool andproducts derived from it. Thus, there is a need to detect the presenceof human parvovirus types 1, 2 and 3 in biological samples, such asdonated blood or plasma to prevent further infection. Further, there isa need that detection assays provide a detection sensitivity that allowsfor detection of low titers of virus, as may occur early in an infectionor in diluted or pooled samples. Parvovirus nucleic acid detectionassays that can detect an appropriate level of contamination mayfacilitate removal of infected donated units from the blood supply orcontaminated lots of pooled plasma before use.

Many immunodiagnostic methods detect anti-parvovirus antibodies (IgM orIgG) present in an individual's serum or plasma (e.g., see PCT Nos. WO96/09391 by Wolf et al. and WO 96/27799 by Hedman et al.). These methodshave limitations in detecting recent or current infections because theyrely on detecting the body's response to the infectious agent. The rapidrise in viremia following infection results in high levels of parvovirusin an individual's blood without corresponding detectable levels ofanti-parvovirus antibodies (See, e.g., U.S. Pat. No. 7,094,541 toBentano et al at Example 4). Thus, immunological-based detection assaysare susceptible to false negative results. Furthermore, viremia is oftenquickly cleared, yet a person may remain antibody-positive in theabsence of these infective particles, thusly leading to false positiveresults. As many as 90% of adults are seropositive for parvovirus,making accurate immunological detection of recent or current infectionsdifficult. Other similar assays detect the presence of parvovirus bydetecting the virus or empty viral capsid bound to a purified cellularreceptor (U.S. Pat. No. 5,449,608 to Young et al.), and theseimmuno-based assays experience similar problems.

DNA hybridization and amplification methods have also been used todetect human parvovirus, though these tests are generally directed tothe detection of genotype 1 only. Yet, U.S. and European regulatorybodies have promulgated standards specifying that plasma pools used formanufacturing anti-D immunoglobulin and other plasma derivatives cancontain no more than 10,000 IU/ml (10 IU/microliter in Europe) of anyhuman parvovirus. As discussed above, therapeutic plasma pools anddiagnostic tests need similarly to reliably identify human parvovirustypes 1, 2 and 3. Thus, there is a need in the art for compositions,kits and methods useful in the in vitro nucleic acid detection of humanparvovirus types 1, 2 and 3.

SUMMARY OF THE INVENTION

The present invention relates to compositions, kits and methods for thedetection of human parvovirus genotypes 1, 2 and 3. These compositions,kits and methods are configured to amplify target sequences of humanparvovirus nucleic acids and are configured to detect target sequencesof human parvovirus nucleic acids or amplified nucleic acids. In certainembodiments and aspects, particular regions within target sequences ofthe human parvovirus have been identified as preferred targets fornucleic acid amplification reactions of a sample, including biologicalspecimens derived from infected humans Amplification oligomers ordetection oligomers targeting these regions may share common coresequences, and thus provide a plurality of particularly preferredamplification oligomers or detection oligomers Amplification productsgenerated using such particularly preferred amplification oligomers willcontain target specific sequences useful for specific detection of humanparvovirus from a sample. Detection of an amplification product caninclude any of a variety of methods, including, but not limited to,probe-based detection, hybridization protection assays, molecular torch,molecular beacon or molecular switch based assays, mass spectrometry,MALDI-TOF mass spectrometry, ESI-TOF mass spectrometry, real-timedetection assays, gel-electrophoresis, SDS-PAGE electrophoresis and thelike. These preferred regions of a target sequence provide improvementsin relation to specificity, sensitivity, or speed of detection ofgenotype 1, as well as the ability to quickly and specifically detectgenotypes 2 and 3 with high sensitivity. Using these amplificationand/or detection oligomers, the methods include the steps of amplifyingtarget sequences within human parvovirus genome and detecting theamplification products. Detection oligomers are preferably used fordetecting amplified products.

In describing the preferred regions within a target sequence of a humanparvovirus nucleic acid, reference is made to GenBank Accession No.DQ225149.1 gi:77994407, entered at GenBank on Oct. 26, 2005 withnon-sequence related updates on Sep. 12, 2006. This accession number isprovided in the sequence listing as SEQ ID NO:90. When discussingregions within a target sequence, the regions are referred to ascorresponding to certain residues of SEQ ID NO:90. Such regions aregiven their own SEQ ID NOS and are provided in the sequence listing.Similarly, amplification oligomer combinations are sometimes referred toas being configured to generate from SEQ ID NO:90 amplicons containingtarget specific sequences, which are portions of the target sequence.One of ordinary skill in the art will understand that these referencesto SEQ ID NO:90 are provided for convenience in describing the currentcompositions, kits and methods. The ordinarily skilled artisanunderstands that such a reference for convenience does not limit thecurrent compositions, kits and methods to use only with SEQ ID NO:90,but rather these compositions, kits and methods are broadly useful forthe amplification and/or detection of human parvovirus genotypes 1, 2 or3.

An embodiment provides an amplification oligomer combination comprisingat least one primer oligomer member and at least one promoter-basedoligomer member comprising a target binding sequence from 10-40nucleobases in length and configured to specifically hybridize to all ora portion of a region of a target sequence of a human parvovirus nucleicacid, said region corresponding to residue 2428 to residue 2438 ofGenBank Accession No. DQ225149.1 gi:77994407 (SEQ ID NO:83); whereinthis amplification oligomer combination is configured to generate fromGenBank Accession No. DQ225149.1 gi:77994407 an amplicon that is about100 nucleobases in length to about 225 nucleobases in length andcomprises a target specific sequence that that contains SEQ ID NO:39. Inone aspect of this embodiment, the amplicon further comprises anon-target specific sequence selected from the group consisting of a tagsequence, an insert sequence, a promoter sequence that is SEQ ID NO:19,SEQ ID NO:94, SEQ ID NO:95 and combinations thereof.

In one aspect of this embodiment, the amplification oligomer combinationis configured to generate from GenBank Accession No. DQ225149.1gi:77994407 an amplicon that is about 100 nucleobases in length to about225 nucleobases in length and comprises a target specific sequence thatthat contains SEQ ID NO:99. In another aspect of this embodiment, theamplification oligomer combination is configured to generate an ampliconcomprising a target specific sequence that contains SEQ ID NO:86. Inanother aspect of this embodiment, the amplification oligomercombination is configured to generate an amplicon comprising a targetspecific sequence that contains SEQ ID NO:87. In another aspect of thisembodiment, the amplification oligomer combination is configured togenerate an amplicon comprising a target specific sequence that containsSEQ ID NO:100. In another aspect of this embodiment, the amplificationoligomer combination is configured to generate an amplicon comprising atarget specific sequence that contains SEQ ID NO:25. In another aspectof this embodiment, the amplification oligomer combination is configuredto generate an amplicon comprising a target specific sequence thatcontains SEQ ID NO:88. In another aspect of this embodiment, theamplification oligomer combination is configured to generate an ampliconcomprising a target specific sequence that contains SEQ ID NO:89. Inanother aspect of this embodiment, the amplification oligomercombination is configured to generate an amplicon comprising a targetspecific sequence that contains SEQ ID NO:26. In another aspect of thisembodiment, the amplification oligomer combination is configured togenerate an amplicon comprising a target specific sequence that containsSEQ ID NO:98. In another aspect of this embodiment, the amplificationoligomer combination is configured to generate an amplicon comprising atarget specific sequence that is 90% identical to SEQ ID NO:88. Inanother aspect of this embodiment, the amplification oligomercombination is configured to generate an amplicon comprising a targetspecific sequence that is 95% identical to SEQ ID NO:88. In anotheraspect of this embodiment, the amplification oligomer combination isconfigured to generate an amplicon comprising a target specific sequencethat is 90% identical to SEQ ID NO:88 and that contains SEQ ID NO:96.

In a further aspect of this embodiment, the at least one primer oligomermember comprises a target binding sequence configured to specificallyhybridize to all or a portion of a region of a target sequence of ahuman parvovirus nucleic acid said region corresponding to residues 2304to 2332 of GenBank Accession No. DQ225149.1 gi:77994407 (SEQ ID NO:96).In another aspect of this embodiment, the at least one primer oligomermember comprises a target binding sequence configured to specificallyhybridize to all or a portion of a region of a target sequence of ahuman parvovirus nucleic acid said region corresponding to residues 2302to 2319 of GenBank Accession No. DQ225149.1 gi:77994407 (SEQ ID NO:38).In another aspect of this embodiment, the at least one primer oligomermember comprises a target binding sequence configured to specificallyhybridize to all or a portion of a region of a target sequence of ahuman parvovirus nucleic acid said region corresponding to residues 2298to 2332 of GenBank Accession No. DQ225149.1 gi:77994407 (SEQ ID NO:35).In another aspect of this embodiment, the at least one primer oligomermember further comprises a 5′ tag sequence. In another aspect of thisembodiment, the at least one primer member is selected from the groupconsisting of SEQ ID NO:18, SEQ ID NO:47, SEQ ID NO:48, SEQ ID NO:49,SEQ ID NO:50 and combinations thereof. In a particular aspect of thisembodiment, the at least one primer member is SEQ ID NO:50. In aparticular aspect of this embodiment, the at least one primer member isSEQ ID NO:47.

In a further aspect of this embodiment, the amplification oligomercombination comprises at least one primer oligomer member comprising atarget binding sequence configured to specifically hybridize to all or aportion of a region of a target sequence of a human parvovirus nucleicacid said region corresponding to residues 2308 to 2332 of GenBankAccession No. DQ225149.1 gi:77994407 (SEQ ID NO:96), and wherein saidamplification oligomer combination is configured to generate an ampliconthat comprises a target specific sequence that contains SEQ ID NO:99. Inanother aspect of this embodiment, said primer member is selected fromthe group consisting of SEQ ID NOS:18, 47, 48, 49 and 50. In anotheraspect of this embodiment, said primer oligomer member is SEQ ID NO:50.In another aspect of this embodiment, said primer oligomer member is SEQID NO:47. In another aspect of this embodiment, said promoter-basedoligomer member comprises a target binding sequence containing SEQ IDNO:84. In another aspect of this embodiment, said promoter-basedoligomer member is configured to specifically hybridize with all or aportion of a region within a target sequence of a human parvovirusnucleic acid, said region corresponding to residues 2414 to 2449 ofGenBank Accession No. DQ225149.1 gi:77994407 (SEQ ID NO:85).

In a further aspect of this embodiment, the at least one promoter-basedoligomer member is configured to specifically hybridize with all or aportion of a region of a target sequence of a human parvovirus nucleicacid, said region corresponding to SEQ ID NO:85. In another aspect ofthis embodiment, the at least one promoter based oligomer membercomprises a target binding sequence containing SEQ ID NO:84. In anotheraspect of this embodiment, the at least one promoter-based oligomermember comprises a target binding sequence selected from the groupconsisting of SEQ ID NO:24, SEQ ID NO:57; SEQ ID NO:60, SEQ ID NO:62,SEQ ID NO:70, SEQ ID NO:75, SEQ ID NO:80 and combinations thereof. In aparticular aspect of this embodiment, the at least one promoter-basedoligomer member comprises a target binding sequence that is SEQ IDNO:75. In a particular aspect of this embodiment, the at least onepromoter-based oligomer member comprises a target binding sequence thatis SEQ ID NO:80. In a particular aspect of this embodiment, the at leastone promoter based oligomer member is a first promoter-based oligomermember comprising a target binding sequence that is SEQ ID NO:75 and asecond promoter-based oligomer member comprising a target bindingsequence that is SEQ ID NO:80. In another aspect of this embodiment, theat least one promoter-based oligomer member is selected from the groupconsisting of SEQ ID NO:23, SEQ ID NO:56, SEQ ID NO:61. SEQ ID NO:66,SEQ ID NO:72, SEQ ID NO:76, SEQ ID NO:81 and combinations thereof. In aparticular aspect of this embodiment, the at least one promoter-basedoligomer member is SEQ ID NO:76. In a particular aspect of thisembodiment, the at least one promoter-based oligomer member comprises atarget binding sequence that is SEQ ID NO:81. In a particular aspect ofthis embodiment, the at least one promoter based oligomer member is afirst promoter-based oligomer member comprising a target bindingsequence that is SEQ ID NO:76 and a second promoter-based oligomermember comprising a target binding sequence that is SEQ ID NO:81. In afurther aspect of this embodiment, the at least one promoter-basedoligomer member further comprises an internal tag sequence. In anotheraspect of this embodiment, the at least one promoter based oligomer isselected from the group consisting of SEQ ID NOS:58, 63, 67, 68, 73, 78,82 and combinations thereof. In a particular aspect of this embodiment,the at least one promoter based oligomer is SEQ ID NO:73. In aparticular aspect of this embodiment, the at least one promoter basedoligomer is SEQ ID NO:78. In a particular aspect of this embodiment, theat least one promoter based oligomer member is a first promoter-basedoligomer member comprising a target binding sequence that is SEQ IDNO:73 and a second promoter-based oligomer member comprising a targetbinding sequence that is SEQ ID NO:78.

In a further aspect of this embodiment, the at least one primer oligomermember is SEQ ID NO:50 and the at least one promoter-based oligomermember is selected from the group comprising SEQ ID NOS:73, 75, 76, 78,80, 81 and combinations thereof. In a particular aspect of thisembodiment, the at least one primer oligomer member is SEQ ID NO:50 andthe at least one promoter-based oligomer member is SEQ ID NOS:73 and 78.In another aspect of this embodiment, the at least one primer oligomermember is SEQ ID NO:47 and the at least one promoter-based oligomermember is selected from the group comprising SEQ ID NOS:73, 75, 76, 78,80, 81 and combinations thereof. In a particular aspect of thisembodiment, the at least one primer oligomer member is SEQ ID NO:47 andthe at least one promoter-based oligomer member is SEQ ID NOS:73 and 78.

In a further aspect of this embodiment there is provided at least oneprimer oligomer member comprising a target binding sequence configuredto specifically hybridize to all or a portion of a region of a targetsequence of a human parvovirus nucleic acid, wherein said regioncorresponds to residues 2304-2332 of GenBank Accession No. DQ225149.1gi:77994407 (SEQ ID NO:96), and wherein said amplification oligomercombination is configured to generate from GenBank Accession No.DQ225149.1 gi:77994407 and amplicon comprising a target specificsequence that contains SEQ ID NO:99. In another aspect, the primeroligomer member is selected from the group consisting of SEQ ID NOS:18,47, 48, 49 and 50. In another aspect, the primer oligomer member is SEQID NO:50. In another aspect, the primer oligomer member is SEQ ID NO:47.In another aspect, the amplification oligomer combination comprisespromoter-based oligomer member comprising a target binding sequencecontaining SEQ ID NO:84. In another aspect, the amplification oligomercombination comprises promoter-based oligomer member configured tospecifically hybridize with all or a portion of a region within a humanparvovirus nucleic acid, said region corresponding to SEQ ID NO:85.

In another embodiment there is provided a method for the detection ofhuman parvovirus from a sample comprising the steps of: obtaining asample suspected of containing human parvovirus type1, type 2, or type3; contacting said sample with an amplification oligomer combination;wherein the amplification oligomer combination comprises at least oneprimer oligomer member and at least one promoter-based oligomer membercomprising a target binding sequence from 10-40 nucleobases in lengthand configured to specifically hybridize to a region of a target nucleicacid of a human parvovirus, said region corresponding to residues 2428to 2438 of GenBank Accession No. DQ225149.1 gi:77994407 (SEQ ID NO:83);wherein this amplification oligomer combination is configured togenerate from said GenBank Accession No. DQ225149.1 gi:77994407 anamplicon that is about 100 nucleobases in length to about 225nucleobases in length and that comprises a target specific sequence thatcontains SEQ ID NO:39; performing an amplification reaction on saidsample to generate an amplicon from a human parvovirus in said sample;and detecting said amplicon; wherein the presence of an amplicon asdetermined by said detecting step indicates that one or more of humanparvovirus genotypes types 1, 2 or 3 are present in said sample.

In one aspect of this embodiment, the amplification oligomer combinationis configured to generate an amplicon comprising a target specificsequence containing SEQ ID NO:99. In another aspect of this embodiment,the amplification oligomer combination is configured to generate anamplicon containing SEQ ID NO:86. In another aspect of this embodiment,the amplification oligomer combination is configured to generate anamplicon containing SEQ ID NO:87. In another aspect of this embodiment,the amplification oligomer combination is configured to generate anamplicon containing SEQ ID NO:100. In another aspect of this embodiment,the amplification oligomer combination is configured to generate anamplicon containing SEQ ID NO:25. In another aspect of this embodiment,the amplification oligomer combination is configured to generate anamplicon containing SEQ ID NO:88. In another aspect of this embodiment,the amplification oligomer combination is configured to generate anamplicon containing SEQ ID NO:89. In another aspect of this embodiment,the amplification oligomer combination is configured to generate anamplicon comprising a target specific sequence containing SEQ ID NO:26.In another aspect of this embodiment, the amplification oligomercombination is configured to generate an amplicon containing SEQ IDNO:98. In another aspect of this embodiment, the amplification oligomercombination is configured to generate an amplicon comprising a targetspecific sequence that is 90% identical to SEQ ID NO:88. In anotheraspect of this embodiment, the amplification oligomer combination isconfigured to generate an amplicon comprising a target specific sequencethat is 95% identical to SEQ ID NO:88. In another aspect of thisembodiment, the amplification oligomer combination is configured togenerate an amplicon comprising a target specific sequence that is 90%identical to SEQ ID NO:88 and that contains SEQ ID NO:96.

In a further aspect of this embodiment, the at least one primer oligomermember comprises a target binding sequence configured to specificallyhybridize to all or a portion of a region within a target sequence of ahuman parvovirus nucleic acid, wherein said region corresponds toresidues 2304 to 2332 of GenBank Accession No. DQ225149.1 gi:77994407(SEQ ID NO:96). In another aspect of this embodiment, the at least oneprimer oligomer member further comprises a 5′ tag sequence. In anotheraspect of this embodiment, the at least one primer member is selectedfrom the group consisting of SEQ ID NO:18, SEQ ID NO:47, SEQ ID NO:48,SEQ ID NO:49, SEQ ID NO:50 and combinations thereof. In a particularaspect of this embodiment, the at least one primer member is SEQ IDNO:50. In a particular aspect of this embodiment, the at least oneprimer member is SEQ ID NO:47.

In a further aspect of this embodiment, the at least one promoter-basedoligomer member is configured to specifically hybridize with all or aportion of a region within a target sequence of a human parvovirusnucleic acid, said region corresponding to residue 2414 to residue 2449of GenBank Accession No. DQ225149.1 gi:77994407 (SEQ ID NO:85). Inanother aspect of this embodiment, the at least one promoter-basedoligomer member comprises a target binding sequence containing SEQ IDNO:84. In another aspect of this embodiment, the at least onepromoter-based oligomer member is configured to specifically hybridizewith all or a portion of a region within a target sequence of a humanparvovirus nucleic acid, said region corresponding to residue 2428 toresidue 2449 of said GenBank Accession No. DQ225149.1 gi:77994407 (SEQID NO:97). In another aspect of this embodiment, the at least onepromoter-based oligomer member comprises a target binding sequenceselected from the group consisting of SEQ ID NO:24, SEQ ID NO:57; SEQ IDNO:60, SEQ ID NO:62, SEQ ID NO:70, SEQ ID NO:75, SEQ ID NO:80 andcombinations thereof. In a particular aspect of this embodiment, the atleast one promoter-based oligomer member comprises a target bindingsequence that is SEQ ID NO:75. In a particular aspect of thisembodiment, the at least one promoter-based oligomer member comprises atarget binding sequence that is SEQ ID NO:80. In a particular aspect ofthis embodiment, the at least one promoter based oligomer member is afirst promoter-based oligomer member comprising a target bindingsequence that is SEQ ID NO:75 and a second promoter-based oligomermember comprising a target binding sequence that is SEQ ID NO:80. Inanother aspect of this embodiment, the at least one promoter-basedoligomer member is selected from the group consisting of SEQ ID NO:23,SEQ ID NO:56, SEQ ID NO:61. SEQ ID NO:66, SEQ ID NO:72, SEQ ID NO:76 andcombinations thereof. In a particular aspect of this embodiment, the atleast one promoter-based oligomer member is SEQ ID NO:76. In aparticular aspect of this embodiment, the at least one promoter-basedoligomer member comprises a target binding sequence that is SEQ IDNO:81. In a particular aspect of this embodiment, the at least onepromoter based oligomer member is a first promoter-based oligomer membercomprising a target binding sequence that is SEQ ID NO:76 and a secondpromoter-based oligomer member comprising a target binding sequence thatis SEQ ID NO:81. In a further aspect of this embodiment, the at leastone promoter-based oligomer member further comprises an internal tagsequence. In another aspect of this embodiment, the at least onepromoter based oligomer is selected from the group consisting of SEQ IDNOS:58, 63, 67, 68, 73, 78 and combinations thereof. In a particularaspect of this embodiment, the at least one promoter based oligomer isSEQ ID NO:73. In a particular aspect of this embodiment, the at leastone promoter based oligomer is SEQ ID NO:78. In a particular aspect ofthis embodiment, the at least one promoter based oligomer member is afirst promoter-based oligomer member comprising a target bindingsequence that is SEQ ID NO:73 and a second promoter-based oligomermember comprising a target binding sequence that is SEQ ID NO:78.

In a further aspect of this embodiment, the at least one primer oligomermember is SEQ ID NO:50 and the at least one promoter-based oligomermember is selected from the group comprising SEQ ID NOS:73, 75, 76, 78,80, 81 and combinations thereof. In a particular aspect of thisembodiment, the at least one primer oligomer member is SEQ ID NO:50 andthe at least one promoter-based oligomer member is SEQ ID NOS:73 and 78.In another aspect of this embodiment, the at least one primer oligomermember is SEQ ID NO:47 and the at least one promoter-based oligomermember is selected from the group comprising SEQ ID NOS:73, 75, 76, 78,80, 81 and combinations thereof. In a particular aspect of thisembodiment, the at least one primer oligomer member is SEQ ID NO:47 andthe at least one promoter-based oligomer member is SEQ ID NOS:73 and 78.

In a further aspect of this embodiment there is provided at least oneprimer oligomer member comprising a target binding sequence configuredto specifically hybridize to all or a portion of a region of a targetsequence of a human parvovirus nucleic acid, wherein said regioncorresponds to residues 2304-2332 of GenBank Accession No. DQ225149.1gi:77994407 (SEQ ID NO:96), and wherein said amplification oligomercombination is configured to generate from GenBank Accession No.DQ225149.1 gi:77994407 and amplicon comprising a target specificsequence that contains SEQ ID NO:99. In another aspect, the primeroligomer member is selected from the group consisting of SEQ ID NOS:18,47, 48, 49 and 50. In another aspect, the primer oligomer member is SEQID NO:50. In another aspect, the primer oligomer member is SEQ ID NO:47.In another aspect, the amplification oligomer combination comprisespromoter-based oligomer member comprising a target binding sequencecontaining SEQ ID NO:84. In another aspect, the amplification oligomercombination comprises promoter-based oligomer member configured tospecifically hybridize with all or a portion of a region within a targetsequence of human parvovirus nucleic acid, said region corresponding toSEQ ID NO:85.

In a further aspect of this embodiment, the detecting step is ahybridization protection assay that utilizes a detection probe that is15 to 40 nucleobases in length and comprises a target binding sequenceconfigured to specifically hybridize to all or a portion of a regionwithin a target sequence of human parvovirus amplified nucleic acid,said region corresponding to residues 2376 to 2409 of GenBank AccessionNo. DQ225149.1 gi:77994407 (SEQ ID NO:33). In another aspect of thisembodiment, detection probe comprises a target binding sequenceconfigured to specifically hybridize to all or a portion of a regionwithin a target sequence of human parvovirus amplified nucleic acid,said region corresponding to residues 2379 to 2396 of GenBank AccessionNo. DQ225149.1 gi:77994407 (SEQ ID NO:40). In another aspect of thisembodiment, the detection probe comprises a target binding sequence thatcontains 5′-GTGAAGAC-3′. In another aspect of this embodiment, thedetection probe is substantially similar to a detection probe selectedfrom the group consisting of: SEQ ID NOS:28, 30, 31, 32, 42, 43, 44 and46. In a particular aspect of this embodiment, the detection probe isSEQ ID NO:42.

In a particular aspect of this embodiment, the at least one primeroligomer member is SEQ ID NO:47, and the at least one promoter-basedoligomer member is SEQ ID NOS:73 and 78, and the detecting step is ahybridization protection assay that utilizes a detection probe that isSEQ ID NO:42. In a particular aspect of this embodiment, the at leastone primer oligomer member that is SEQ ID NO:50 and the at least onepromoter-based oligomer member is SEQ ID NOS:73 and 78, and thedetecting step is a hybridization protection assay that utilizes adetection probe that is SEQ ID NO:42.

It should be understood that both the foregoing general description andthe following detailed description are exemplary only and are notrestrictive of the invention. The detailed description and examplesillustrate various embodiments and explain the principles of theinvention.

DETAILED DESCRIPTION OF THE INVENTION

This application discloses oligonucleotide sequences configured for useas amplification oligomers and detection probe oligomers for detectingby an in vitro nucleic acid amplification assay parvovirus types 1, 2and 3 nucleic acid sequences present in a biological sample. Anembodiment of the method uses transcription-mediated nucleic acidamplification (as previously disclosed in detail in U.S. Pat. Nos.5,399,491 and 5,554,516 to Kacian et al.). Methods for detectingamplified nucleic acid use sequence-specific probes that hybridizespecifically to a portion of the amplified sequences. In one aspect, themethod uses any known homogeneous detection step to detect, in amixture, a labeled probe that is bound to an amplified nucleic acid(e.g., as disclosed by Arnold et al., Clin. Chem. 35:1588-1594 (1989);U.S. Pat. No. 5,658,737 to Nelson et al., and U.S. Pat. Nos. 5,118,801and 5,312,728 to Lizardi et al.). This application also disclosesoligonucleotide sequences that are useful for capturing parvovirus types1, 2 and 3 target DNA by using nucleic acid hybridization techniques.One embodiment of the capturing step uses magnetic particles to separatethe captured target (see U.S. Pat. No. 6,110,678 to Weisburg et al.).

It is to be noted that the term “a” or “an” entity refers to one or moreof that entity; for example, “a nucleic acid,” is understood torepresent one or more nucleic acids. As such, the terms “a” (or “an”),“one or more,” and “at least one” can be used interchangeably herein.

By “biological sample” is meant any tissue or material derived from aliving or dead human which may contain parvovirus nucleic acid,including, for example, sputum, peripheral blood, plasma, serum, biopsytissue including lymph nodes, respiratory tissue or exudates, or otherbody fluids, tissues or materials. The sample may be treated tophysically, chemically and/or mechanically disrupt tissue or cellstructure, thus releasing intracellular components. Sample preparationmay use a solution that contains buffers, salts, detergents and the likewhich are used to prepare the sample for analysis.

By “nucleic acid” is meant a multimeric compound comprising two or morecovalently bonded nucleosides or nucleoside analogs which havenitrogenous heterocyclic bases, or base analogs, linked together bynucleic acid backbone linkages (e.g., phosphodiester bonds) to form apolynucleotide. Conventional RNA and DNA are included in the term“nucleic acid” as are analogs thereof. The nucleic acid backbone mayinclude a variety of linkages, for example, one or more ofsugar-phosphodiester linkages, peptide-nucleic acid bonds (see PCT No.WO 95/32305 by Hydig-Hielsen et al.), phosphorothioate ormethylphosphonate linkages or mixtures of such linkages in a singleoligonucleotide. Sugar moieties in the nucleic acid may be either riboseor deoxyribose, or similar compounds with known substitutions, such as,for example, 2′ methoxy substitutions and 2′ halide substitutions (e.g.,2′-F). Conventional nitrogenous bases (A, G, C, T, U), known baseanalogs (e.g., inosine; see The Biochemistry of the Nucleic Acids 5-36,Adams et al., ed., 11^(th) ed., 1992), derivatives of purine orpyrimidine bases (e.g., N⁴-methyl deoxygaunosine, deaza- or aza-purinesand deaza- or aza-pyrimidines, pyrimidines having a substituent at the 5or 6 positions, purine bases having a substituent at the 2, 6 or 8positions, 2-amino-6-methylaminopurine, O⁶-methylguanine,4-thio-pyrimidines, 4-amino-pyrimidines,4-dimethylhydrazine-pyrimidines, and O⁴-alkyl-pyrimidines; PCT No. WO93/13121 by Cook) and “abasic” residues (i.e., no nitrogenous base forone or more backbone positions) (U.S. Pat. No. 5,585,481 to Arnold etal.) are included in the term nucleic acid. That is, a nucleic acid maycomprise only conventional sugars, bases and linkages found in RNA andDNA, or may include both conventional components and substitutions(e.g., conventional bases and analogs linked via a methoxy backbone, orconventional bases and one or more base analogs linked via an RNA or DNAbackbone). Another non-limiting example of a nucleic acid analogcontemplated by the present invention includes bicyclic and tricyclicnucleoside and nucleotide configurations (Locked Nucleic Acids,” “LockedNucleoside Analogues” or “LNA”. See Imanishi et al., U.S. Pat. No.6,268,490; and Wengel et al., U.S. Pat. No. 6,670,461.)

The backbone of an oligomer may affect stability of a hybridizationcomplex (e.g., formed between of a capture oligomer to its targetnucleic acid). Such embodiments include peptide linkages, 2′-O-methoxylinkages and sugar-phosphodiester type linkages. Peptide nucleic acidsare advantageous for forming a hybridization complex with RNA. Anoligomer having 2′-methoxy substituted RNA groups or a 2′-fluorosubstituted RNA may have enhance hybridization complex stabilityrelative to standard DNA or RNA and is preferred for forming ahybridization complex with a complementary 2′-OH RNA. A linkage joiningtwo sugar groups may affect hybridization complex stability by affectingthe overall charge or the charge density, or by affecting stericinteractions (e.g., bulky linkages may reduce hybridization complexstability). Preferred linkages include those with neutral groups (e.g.,methylphosphonates) or charged groups (e.g., phosphorothioates) toaffect complex stability.

The term “polynucleotide” as used herein denotes a nucleic acid chain.Throughout this application, nucleic acids are designated by the5′-terminus to the 3′-terminus. Standard nucleic acids, e.g., DNA andRNA, are typically synthesized “3′-to-5′,” i.e., by the addition ofnucleotides to the 5′-terminus of a growing nucleic acid.

A “nucleotide” as used herein is a subunit of a nucleic acid consistingof a phosphate group, a 5-carbon sugar and a nitrogenous base. The5-carbon sugar found in RNA is ribose. In DNA, the 5-carbon sugar is2′-deoxyribose. The term also includes analogs of such subunits, such asa methoxy group at the 2′ position of the ribose (2′-O-Me). As usedherein, methoxy oligonucleotides containing “T” residues have a methoxygroup at the 2′ position of the ribose moiety, and a uracil at the baseposition of the nucleotide.

A “non-nucleotide unit” as used herein is a unit that does notsignificantly participate in hybridization of a polymer. Such units mustnot, for example, participate in any significant hydrogen bonding with anucleotide, and would exclude units having as a component one of thefive nucleotide bases or analogs thereof.

By “oligonucleotide” or “oligomer” is meant a nucleic acid havinggenerally less than 1,000 residues, including polymers in a size rangehaving a lower limit of about 5 nucleotide residues and an upper limitof about 500 nucleotide residues. Oligomers of some embodiments of theinvention are in a size range having a lower limit of about 5 to about15 residues and an upper limit of about 50 to 100 residues. Embodimentsof oligomers are in a size range having a lower limit of about 10 toabout 25 residues and an upper limit of about 25 to about 60 residues.These ranges are inclusive, such that all whole numbers in between arealso disclosed. Oligomers may be purified from naturally occurringsources, but generally are synthesized in vitro by using any well-knownenzymatic or chemical method. Generally, when an oligomer of the presentinvention is synthesized in vitro with a 2′-O-methoxy backbone, a uracil(U) base is used in those positions that are occupied by a thymine (T)base in the same sequence in an oligomer synthesized withsugar-phosphodiester linkages, except for a 3′ T, which is a standarddeoxynucleotide. That is, methoxy oligonucleotides have a methoxy groupat the 2′ position of the ribose moiety, and a U at the base position ofa T residue in a standard DNA oligonucleotide, except when a T ispresent at the 3′ end of the oligomer. When an oligomer is specified ascontaining an “OMeT” residue, a T residue occupies the base position andthe backbone comprises 2′-O-methoxy linkages. Although an oligomer basesequence frequently is referred to as a DNA sequence (i.e., contains Tresidues), one skilled in the art will appreciate that the correspondingRNA sequence (i.e., the same base sequence but containing U in place ofT), or the complementary DNA or RNA sequences are substantiallyequivalent embodiments of the specified DNA sequence. Indeed, asdescribed above, an oligomer with a 2′-O-methoxy backbone may contain amixture of U and T bases in the same oligomer.

By “amplification oligonucleotide” or “amplification oligomer” is meantan oligonucleotide, at least the 3′-end of which is complementary to atarget nucleic acid, and which hybridizes to a target nucleic acid, orits complement, and participates in nucleic acid amplification. Forsimplicity, amplification oligomers discussed herein will refer tohybridizing to a target nucleic acid sequence. However, as is understoodby those ordinarily skilled in the art, such amplification oligomers canbe configured to hybridize the referenced nucleic acid sequence or thecomplement thereof. Examples or amplification oligomers include primersand promoter-primers. Preferably, an amplification oligonucleotidecontains at least 10 contiguous bases, and more preferably at leastabout 12 contiguous bases but less than about 70 bases, that hybridizespecifically with a region of the target nucleic acid sequence understandard hybridization conditions. The contiguous bases that hybridizeto the target sequence are at least about 80%, preferably at least about90%, and more preferably about 100% complementary to the sequence towhich the amplification oligonucleotide hybridizes. An amplificationoligonucleotide optionally may include modified nucleotides.

Amplification oligomers may be referred to as “primers” or“promoter-primers.” A “primer” refers to an oligonucleotide thathybridizes to a template nucleic acid and has a 3′ end that can beextended in a known polymerization reaction. The 5′ region of the primermay be non-complementary to the target nucleic acid, e.g., the 5′non-complementary region may include a promoter sequence and theoligomer is referred to as a “promoter-primer.” As used herein, a“promoter” is a specific nucleic acid sequence that is recognized by aDNA-dependent RNA polymerase (“transcriptase”) as a signal to bind tothe nucleic acid and begin the transcription of RNA at a specific site.Further, promoter primers may comprise blocked 3′ ends to prevent theiruse as a primer, and in these instances, the amplification oligomer isreferred to as a promoter provider. In some embodiments, blockingmoieties replace an oligomer's 3′OH to prevent enzyme-mediated extensionof the oligomer in an amplification reaction. In alternative embodimentsa blocking moiety may be within five residues of the 3′ end and issufficiently large to limit binding of a polymerase to the oligomer. Inother embodiments a blocking moiety is covalently attached to the 3′terminus of an oligomer. Many different chemical groups may be used toblock the 3′ end of an oligomer, including, but not limited to, alkylgroups, non-nucleotide linkers, alkane-diol dideoxynucleotide residues,and cordycepin. Those skilled in the art will further appreciate thatany oligomer that can function as a primer (i.e., an amplificationoligonucleotide that hybridizes specifically to a target sequence andhas a 3′ end that can be extended by a polymerase) can be modified toinclude a 5′ promoter sequence, and thus function as a promoter-primer.Similarly, any promoter-primer can be modified by removal of, orsynthesis without, a promoter sequence and function as a primer.

A “target nucleic acid” as used herein is a nucleic acid comprising a“target sequence” to be amplified. Target nucleic acids may be DNA orRNA as described herein, and may be either single-stranded ordouble-stranded. The target nucleic acid may include other sequencesbesides the target sequence, which may not be amplified. Typical targetnucleic acids include virus genomes, bacterial genomes, fungal genomes,plant genomes, animal genomes, rRNA, tRNA, or mRNA from viruses,bacteria or eukaryotic cells, mitochondrial DNA, or chromosomal DNA.

By “isolated” it is meant that a sample containing a target nucleic acidis taken from its natural milieu, but the term does not connote anydegree of purification.

The term “target sequence” as used herein refers to the particularnucleotide sequence of the target nucleic acid that is to be amplifiedand/or detected. The “target sequence” includes the complexing sequencesto which oligonucleotides (e.g., priming oligonucleotides and/orpromoter oligonucleotides) complex during the processes of TMA. Wherethe target nucleic acid is originally single-stranded, the term “targetsequence” will also refer to the sequence complementary to the “targetsequence” as present in the target nucleic acid. Where the targetnucleic acid is originally double-stranded, the term “target sequence”refers to both the sense (+) and antisense (−) strands. In choosing atarget sequence, the skilled artisan will understand that a “unique”sequence should be chosen so as to distinguish between unrelated orclosely related target nucleic acids.

“Target binding sequence” is used herein to refer to the portion of anoligomer that is configured to hybridize with a target nucleic acidsequence. Preferably, the target binding sequences are configured tospecifically hybridize with a target nucleic acid sequence. Targetbinding sequences may be 100% complementary to the portion of the targetsequence to which they are configured to hybridize; but not necessarily.Target-binding sequences may also include inserted, deleted and/orsubstituted nucleotide residues relative to a target sequence. Less than100% complementarity of a target binding sequence to a target sequencemay arise, for example, when the target nucleic acid is a pluralitystrains within a species, such as would be the case for an oligomerconfigured to hybridize to the various strains and genotypes of humanparvovirus. It is understood that other reasons exist for configuring atarget binding sequence to have less than 100% complementarity to atarget nucleic acid.

The term “targets a sequence” as used herein in reference to a region ofhuman parvovirus nucleic acid refers to a process whereby anoligonucleotide hybridizes to the target sequence in a manner thatallows for amplification and detection as described herein. In oneembodiment, the oligonucleotide is complementary with the targeted humanparvovirus nucleic acid sequence and contains no mismatches. In anotherembodiment, the oligonucleotide is complementary but contains 1; or 2;or 3; or 4; or 5 mismatches with the targeted human parvovirus nucleicacid sequence. Preferably, the oligonucleotide that hybridizes to thehuman parvovirus nucleic acid sequence includes at least 10 to as manyas 50 nucleotides complementary to the target sequence. It is understoodthat at least 10 and as many as 50 is an inclusive range such that 10,50 and each whole number there between are disclosed. Preferably, theoligomer specifically hybridizes to the target sequence. The term“configured to target a sequence” as used herein means that the targethybridizing region of an amplification oligonucleotide is designed tohave a polynucleotide sequence that could specifically hybridize to thereferenced human parvovirus region. Such an amplificationoligonucleotide is not limited to targeting that sequence only, but israther useful as a composition, in a kit or in a method for targeting ahuman parvovirus target nucleic acid including genotypes 1, 2 and/or 3,as is described herein. The term “configured to” denotes an actualarrangement of the polynucleotide sequence configuration of theamplification oligonucleotide target hybridizing sequence.

The term “region” as used herein refers to a portion of a nucleic acidwherein said portion is smaller than the entire nucleic acid. Forexample, when the nucleic acid in reference is an oligonucleotidepromoter primer, the term “region” may be used refer to the smallerpromoter portion of the entire oligonucleotide. Similarly, and also asexample only, when the nucleic acid is a human parvovirus genome, theterm “region” may be used to refer to a smaller area of the nucleicacid, wherein the smaller area is targeted by one or moreoligonucleotides of the invention. The target binding sequence of anoligonucleotide may hybridize all or a portion of a region. A targetbinding sequence that hybridizes to a portion of a region is one thathybridizes within the referenced region. As another non-limiting exampleof the use of the term region, when the nucleic acid in reference is anamplicon, the term region may be used to refer to the smaller nucleotidesequence identified for hybridization by the target binding sequence ofa probe.

“Amplification” refers to any known procedure for obtaining multiplecopies of a target nucleic acid sequence or its complement or fragmentsthereof, and preferred embodiments amplify the target specifically byusing sequence-specific methods. Known amplification methods include,for example, transcription-mediated amplification, replicase-mediatedamplification, polymerase chain reaction (PCR) amplification, ligasechain reaction (LCR) amplification and strand-displacement amplification(SDA). Replicase-mediated amplification uses self-replicating RNAmolecules, and a replicase such as QB-replicase (e.g., see U.S. Pat. No.4,786,600 to Kramer et al. and PCT No. WO 90/14439). PCR amplificationis well known and uses DNA polymerase, sequence-specific primers andthermal cycling to synthesize multiple copies of the two complementarystrands of DNA or cDNA (e.g., U.S. Pat. Nos. 4,683,195, 4,683,202, and4,800,159 to Mullis et al., and Methods in Enzymology, 1987, Vol. 155:335-350). LCR amplification uses at least four separate oligonucleotidesto amplify a target and its complementary strand by using multiplecycles of hybridization, ligation, and denaturation (EP Patent No. 0 320308). SDA amplifies by using a primer that contains a recognition sitefor a restriction endonuclease which nicks one strand of a hemimodifiedDNA duplex that includes the target sequence, followed by amplificationin a series of primer extension and strand displacement steps (U.S. Pat.No. 5,422,252 to Walker et al.) As illustrated below, preferredembodiments use transcription-associated amplification. It will beapparent to one skilled in the art that method steps and amplificationoligonucleotides of the present invention may be readily adapted to avariety of nucleic acid amplification procedures based on primerextension by a polymerase activity.

Amplification of a “fragment” or “portion” of the target sequence refersto production of an amplified nucleic acid containing less than theentire target region nucleic acid sequence. Such fragments may beproduced by amplifying a portion of the target sequence, e.g., by usingan amplification oligonucleotide that hybridizes to and initiatespolymerization from an internal position in the target sequence.

By “transcription-mediated amplification” (TMA) or“transcription-associated amplification” is meant a nucleic acidamplification that uses an RNA polymerase to produce multiple RNAtranscripts from a nucleic acid template. Transcription-associatedamplification generally employs RNA polymerase and DNA polymeraseactivities, deoxyribonucleoside triphosphates, ribonucleosidetriphosphates, and a promoter-primer, and optionally may include one ormore other amplification oligonucleotides, including “helper” oligomers.Variations of transcription-associated amplification are well known inthe art and described in detail elsewhere (see U.S. Pat. Nos. 5,399,491and 5,554,516 to Kacian et al., U.S. Pat. No. 5,437,990 to Burg et al.,U.S. Pat. No. 5,130,238 to Malek et al., U.S. Pat. Nos. 4,868,105 and5,124,246 to Urdea et al., PCT No. WO 93/22461 by Kacian et al., PCTNos. WO 88/01302 and WO 88/10315 by Gingeras et al., PCT No. WO 94/03472by McDonough et al., and PCT No. WO 95/03430 by Ryder et al.). Theprocedures of U.S. Pat. Nos. 5,399,491 and 5,554,516 are preferredamplification embodiments. As used herein, the term “real-time TMA”refers to single-primer transcription-mediated amplification (“TMA”) oftarget nucleic acid that is monitored by real-time detection means.

By “probe,” “detection probe” or “detection probe oligomer” it is meanta nucleic acid oligomer that hybridizes specifically to a targetsequence in a nucleic acid, preferably in an amplified nucleic acid,under conditions that allow hybridization, thereby allowing detection ofthe target or amplified nucleic acid. Detection may either be direct(i.e., resulting from a probe hybridizing directly to the sequence) orindirect (i.e., resulting from a probe hybridizing to an intermediatemolecular structure that links the probe to the target). The probe's“target” generally refers to a sequence within or a subset of anamplified nucleic acid sequence which hybridizes specifically to atleast a portion of a probe oligomer by standard hydrogen bonding (i.e.,base pairing). A probe may comprise target-specific sequences and othersequences that contribute to three-dimensional conformation of the probe(e.g., U.S. Pat. Nos. 5,118,801 and 5,312,728 to Lizardi et al., andU.S. Pat. No. 6,361,945 B1 to Becker et al.). Probes may be DNA, RNA,analogs thereof or combinations thereof and they may be labeled orunlabeled. Probe sequences are sufficiently complementary to theirtarget sequences if they are configured to allow stable hybridization inappropriate hybridization conditions between the probe oligomer and atarget sequence that is not completely complementary to the probe'starget-specific sequence.

By “complementary” is meant that the nucleotide sequences of similarregions of two single-stranded nucleic acids, or to different regions ofthe same single-stranded nucleic acid have a nucleotide base compositionthat allow the single-stranded regions to hybridize together in a stabledouble-stranded hydrogen-bonded region under stringent hybridization oramplification conditions. Sequences that hybridize to each other may becompletely complementary or partially complementary to the intendedtarget sequence by standard nucleic acid base pairing (e.g. G:C, A:T orA:U pairing). By “sufficiently complementary” is meant a contiguoussequence that is capable of hybridizing to another sequence by hydrogenbonding between a series of complementary bases, which may becomplementary at each position in the sequence by standard base pairingor may contain one or more non-complementary residues, including abasicresidues. Sufficiently complementary contiguous sequences typically areat least 80%, or at least 90%, complementary to a sequence to which anoligomer is intended to specifically hybridize. Sequences that are“sufficiently complementary” allow stable hybridization of a nucleicacid oligomer with its target sequence under appropriate hybridizationconditions, even if the sequences are not completely complementary. Whena contiguous sequence of nucleotides of one single-stranded region isable to form a series of “canonical” hydrogen-bonded base pairs with ananalogous sequence of nucleotides of the other single-stranded region,such that A is paired with U or T and C is paired with G, thenucleotides sequences are “completely” complementary, (e.g., Sambrook etal., Molecular Cloning, A Laboratory Manual, 2nd ed. (Cold Spring HarborLaboratory Press, Cold Spring Harbor, N.Y., 1989) at §§ 1.90-1.91,7.37-7.57, 9.47-9.51 and 11.47-11.57, particularly §§ 9.50-9.51,11.12-11.13, 11.45-11.47 and 11.55-11.57).

By “preferentially hybridize” or “specifically hybridize” is meant thatunder stringent hybridization assay conditions, probes hybridize totheir target sequences, or replicates thereof, to form stable probe:target hybrids, while at the same time formation of stable probe:non-target hybrids is minimized Thus, a probe hybridizes to a targetsequence or replicate thereof to a sufficiently greater extent than to anon-target sequence, to enable one having ordinary skill in the art toaccurately quantitate the RNA replicates or complementary DNA (cDNA) ofthe target sequence formed during the amplification. Appropriatehybridization conditions are well known in the art, may be predictedbased on sequence composition, or can be determined by using routinetesting methods (e.g., Sambrook et al., Molecular Cloning, A LaboratoryManual, 2nd ed. (Cold Spring Harbor Laboratory Press, Cold SpringHarbor, N.Y., 1989) at §§ 1.90-1.91, 7.37-7.57, 9.47-9.51 and11.47-11.57, particularly §§ 9.50-9.51, 11.12-11.13, 11.45-11.47 and11.55-11.57).

By “capture oligonucleotide” or “capture oligomer” or “capture probe” ismeant a nucleic acid oligomer that hybridizes specifically to a targetnucleic acid to be captured and provides a means for isolating and/orconcentrating the target from other sample components. Embodiments ofcapture oligomers include two binding regions: a target-binding regionand an immobilized probe-binding region, whereby the capture oligomerforms a hybridization complex in which the target-binding region of thecapture oligomer binds to the target sequence and the immobilizedprobe-binding region binds to an oligomer immobilized on a solid support(see U.S. Pat. Nos. 6,110,678 and 6,280,952 to Weisburg et al.).Although the target-binding region and immobilized probe-binding regionare usually on the same capture oligomer, the two functional regions maybe present on two different oligomers joined together by one or morelinkers. For example, an immobilized probe-binding region may be presenton a first oligomer, a target-binding region may be present on a secondoligomer, and the two oligomers are joined by hydrogen bonding with athird oligomer that is a linker that hybridizes specifically tosequences of the first and second oligomers. The target-binding regionof a capture probe may also be referred to as a target-specific portionof the capture probe and the immobilized probe-binding region may bereferred to as a tail portion. Embodiments of tail portions includehomopolymers (e.g., poly-dT or poly-dA) or non-homopolymers (e.g.,T₁₋₃A₃₀), preferably attached to the 3′ end of the target-specificportion of the oligomer.

By “immobilized probe” or “immobilized oligomer” is meant a nucleic acidoligomer that joins, directly or indirectly, a capture oligomer to animmobilized support. An immobilized probe joined to a solid supportfacilitates separation of bound target sequence from unbound material ina sample. Any known solid support may be used, such as matrices andparticles in solution, e.g., nitrocellulose, nylon, glass, polyacrylate,mixed polymers, polystyrene, silane polypropylene and metal particles,preferably, magnetically attractable particles. Preferred supports aremonodisperse paramagnetic spheres (e.g., uniform size±5%), to provideconsistent results, to which an immobilized probe is joined directly(e.g., via a direct covalent linkage, chelation, or ionic interaction),or indirectly (e.g., via one or more linkers), where the linkage orinteraction is stable during nucleic acid hybridization conditions.

“Sample preparation” refers to any steps or method that treats a samplefor subsequent amplification and/or detection of human parvovirusnucleic acids present in the sample. Samples may be complex mixtures ofcomponents of which the target nucleic acid is a minority component.Sample preparation may include any known method of concentratingcomponents, such as microbes or nucleic acids, from a larger samplevolume, such as by filtration of airborne or waterborne particles from alarger volume sample or by isolation of microbes from a sample by usingstandard microbiology methods. Sample preparation may include physicaldisruption and/or chemical lysis of cellular components to releaseintracellular components into a substantially aqueous or organic phaseand removal of debris, such as by using filtration, centrifugation oradsorption. Sample preparation may include use of a nucleic acidoligonucleotide that selectively or non-specifically capture a targetnucleic acid and separate it from other sample components (e.g., asdescribed in U.S. Pat. No. 6,110,678 and PCT Pub. No. WO 2008/016988).

By “separating” or “purifying” is meant that one or more components ofthe biological sample are removed from at least one other component ofthe sample. Sample components generally include an aqueous solution ofnucleic acids, salts, proteins, carbohydrates, and lipids. A step ofseparating or purifying a nucleic acid removes at least about 70%,preferably at least about 90% and, more preferably, at least about 95%of the other components in the sample.

By “label” is meant a molecular moiety or compound that can be detectedor can lead to a detectable signal. A label is joined, directly orindirectly, to a nucleic acid probe. Direct labeling uses bonds orinteractions that link the label to the probe, including covalent bondsor non-covalent interactions, such as hydrogen bonds, hydrophobic andionic interactions, or through formation of chelates or coordinationcomplexes. Indirect labeling uses a bridging moiety or “linker” (e.g.,oligonucleotide or antibody), to link the label and probe. Linkers canbe used to amplify a detectable signal. Labels are any known detectablemoiety, e.g., radionuclide, ligand (e.g., biotin, avidin), enzyme orenzyme substrate, reactive group, or chromophore, such as a dye ordetectable particle (e.g., latex beads or metal particles), luminescentcompounds (e.g., bioluminescent, phosphorescent or chemiluminescentlabels) and fluorescent compounds. Preferably, the label on a labeledprobe is detectable in a homogeneous reaction (i.e., in a mixture, boundlabeled probe exhibits a detectable change, such as stability ordifferential degradation, compared to unbound labeled probe). Oneembodiment of a label for use in a homogenous assay is achemiluminescent compound (e.g., described in detail in U.S. Pat. No.5,656,207 to Woodhead et al., U.S. Pat. No. 5,658,737 to Nelson et al.,and U.S. Pat. No. 5,639,604 to Arnold, Jr., et al.). Preferredchemiluminescent labels are acridinium ester (AE) compounds, such asstandard AE or derivatives thereof (e.g., naphthyl-AE, ortho-AE, 1- or3-methyl-AE, 2,7-dimethyl-AE, 4,5-dimethyl-AE, ortho-dibromo-AE,ortho-dimethyl-AE, meta-dimethyl-AE, ortho-methoxy-AE,ortho-methoxy(cinnamyl)-AE, ortho-methyl-AE, ortho-fluoro-AE, 1- or3-methyl-ortho-fluoro-AE, 1- or 3-methyl-meta-difluoro-AE, and2-methyl-AE). Synthesis and methods of attaching labels to nucleic acidsand detecting labels are well known in the art (e.g., Sambrook et al.,Molecular Cloning, A Laboratory Manual, 2nd ed. (Cold Spring HarborLaboratory Press, Cold Spring Habor, N Y, 1989), Chapter 10; U.S. Pat.No. 4,581,333 to Kourilsky et al., U.S. Pat. No. 5,658,737 to Nelson etal., U.S. Pat. No. 5,656,207 to Woodhead et al., U.S. Pat. No. 5,547,842to Hogan et al., U.S. Pat. No. 5,283,174 to Arnold, Jr. et al., and EPPatent Pub. No. 0747706 by Becker et al.). Another embodiment of a labelfor use in a homogenous assay is a fluorescent compound attached to aprobe with a quencher compound in functional proximity to thefluorescent label when the probe is not hybridized to its target (e.g.,U.S. Pat. Nos. 5,118,801 and 5,312,728 to Lizardi et al., and 6,361,945B1 to Becker et al.).

A “homogeneous detectable label” refers to a label whose presence can bedetected in a homogeneous fashion based upon whether the labeled probeis hybridized to a target sequence (i.e., can be detected withoutphysically removing unhybridized label or labeled probe). Embodiments ofhomogeneous detectable labels and methods of detecting them have beendescribed (U.S. Pat. No. 5,283,174 to Arnold et al., U.S. Pat. No.5,656,207 to Woodhead et al., U.S. Pat. No. 5,658,737 to Nelson et al.,U.S. Pat. Nos. 5,118,801 and 5,312,728 to Lizardi et al., and6,361,945B1 to Becker et al.).

By “consisting essentially of” is meant that additional component(s) andmethod step(s)] that do not materially change the basic and novelcharacteristics of the present invention may be included. Suchcharacteristics include salts, buffering agents, nucleic acid oligomersand similar biochemical reagents that do not have a material effect onthe characteristics of the claimed components or method steps describedherein that detect parvovirus types 1, 2 and 3 nucleic acid sequences,including nucleic amplification products derived from parvovirus types1, 2 and 3 DNA, with a sensitivity of about 100 to 500 copies of theseparvovirus DNA in the starting material. Similarly, additional methodsteps that do not have a material effect on the basic nature of theassay may be included.

As used herein, an oligonucleotide having a nucleic acid sequence“comprising” or “consisting of” or “consisting essentially of” asequence selected from a group of specific sequences means that theoligonucleotide, as a basic and novel characteristic, is capable ofstably hybridizing to a nucleic acid having the exact complement of oneof the listed nucleic acid sequences of the group under stringenthybridization conditions. An exact complement includes the correspondingDNA or RNA sequence.

As used herein, an oligonucleotide that “corresponds to” or is“corresponding to” a specified nucleic acid sequence means that thereferred to oligonucleotide is sufficiently similar to the referencenucleic acid sequence such that the oligonucleotide has similarhybridization properties to the reference nucleic acid sequence in thatit would hybridize with the same target nucleic acid sequence understringent hybridization conditions. One skilled in the art willunderstand that “corresponding oligonucleotides” can vary from thereferred to sequence and still hybridize to the same target nucleic acidsequence. It is also understood that a first nucleic acid correspondingto a second nucleic acid includes the complements thereof and includesthe RNA and DNA thereof. This variation from the nucleic acid may bestated in terms of a percentage of identical bases within the sequenceor the percentage of perfectly complementary bases between the probe orprimer and its target sequence. Thus, an oligonucleotide “correspondsto” a reference nucleic acid sequence if these percentages of baseidentity or complementarity are from 100% to about 80%. In preferredembodiments, the percentage is from 100% to about 85%. In more preferredembodiments, this percentage can be from 100% to about 90%; in otherpreferred embodiments, this percentage is from 100% to about 95%.Similarly, a region of a nucleic acid or amplified nucleic acid can bereferred to herein as corresponding to a reference nucleic acidsequence. One skilled in the art will understand the variousmodifications to the hybridization conditions that might be required atvarious percentages of complementarity to allow hybridization to aspecific target sequence without causing an unacceptable level ofnon-specific hybridization.

The term “amplicon” or the term “amplification product” as used hereinrefers to the nucleic acid molecule generated during an amplificationprocedure that is complementary or homologous to a sequence containedwithin the target sequence. This complementary or homologous sequence ofan amplicon is sometimes referred to herein as a “target-specificsequence.” Amplicons can be double stranded or single stranded and caninclude DNA, RNA or both. For example, DNA-dependent RNA polymerasetranscribes single stranded amplicons from double stranded DNA duringtranscription-mediated amplification procedures. These single strandedamplicons are RNA amplicons and can be either strand of a doublestranded complex; depending on how the amplification oligomers aredesigned. Thus, amplicons can be single stranded RNA. RNA-dependent DNApolymerases synthesize a DNA strand that is complementary to an RNAtemplate. Thus, amplicons can be double stranded DNA and RNA hybrids.RNA-dependent DNA polymerases often include RNase activity, or are usedin conjunction with an RNase, which degrades the RNA strand. Thus,amplicons can be single stranded DNA. RNA-dependent DNA polymerases andDNA-dependent DNA polymerases synthesize complementary DNA strands fromDNA templates. Thus, amplicons can be double stranded DNA. RNA-dependentRNA polymerases synthesize RNA from an RNA template. Thus, amplicons canbe double stranded RNA. DNA Dependent RNA polymerases synthesize RNAfrom double stranded DNA templates, also referred to as transcription.Thus, amplicons can be single stranded RNA. Amplicons and methods forgenerating amplicons are known to those skilled in the art. Forconvenience herein, a single strand of RNA or a single strand of DNA mayrepresent an amplicon generated by an amplification oligomer combinationof the current invention. Such representation is not meant to limit theamplicon to the representation shown. Skilled artisans in possession ofthe instant disclosure will use amplification oligomers and polymeraseenzymes to generate any of the numerous types of amplicons; all withinthe spirit of the current invention.

A “non-target-specific sequence,” as is used herein refers to a regionof an oligomer sequence, wherein said region does not stably hybridizewith a target sequence under standard hybridization conditions.Oligomers with non-target-specific sequences include, but are notlimited to, promoter primers, and molecular beacons. An amplificationoligomer may contain a sequence that is not complementary to the targetor template sequence; for example, the 5′ region of a primer may includea promoter sequence that is non-complementary to the target nucleic acid(referred to as a “promoter-primer”). Those skilled in the art willunderstand that an amplification oligomer that functions as a primer maybe modified to include a 5′ promoter sequence, and thus function as apromoter-primer. Similarly, a promoter-primer may be modified by removalof, or synthesis without, a promoter sequence and still function as aprimer. A 3′ blocked amplification oligomer may provide a promotersequence and serve as a template for polymerization (referred to as a“promoter provider”). Thus, an amplicon that is generated by anamplification oligomer member such as a promoter primer will comprise atarget-specific sequence and a non-target-specific sequence.

As used herein, the term “relative light unit” (“RLU”) is an arbitraryunit of measurement indicating the relative number of photons emitted bythe sample at a given wavelength or band of wavelengths. RLU varies withthe characteristics of the detection means used for the measurement.

The term “specificity,” in the context of an amplification and/ordetection system, is used herein to refer to the characteristic of thesystem which describes its ability to distinguish between target andnon-target sequences dependent on sequence and assay conditions. Interms of nucleic acid amplification, specificity generally refers to theratio of the number of specific amplicons produced to the number ofside-products (e.g., the signal-to-noise ratio). In terms of detection,specificity generally refers to the ratio of signal produced from targetnucleic acids to signal produced from non-target nucleic acids.

The term “sensitivity” is used herein to refer to the precision withwhich a nucleic acid amplification reaction can be detected orquantitated. The sensitivity of an amplification reaction is generally ameasure of the smallest copy number of the target nucleic acid that canbe reliably detected in the amplification system, and will depend, forexample, on the detection assay being employed, and the specificity ofthe amplification reaction, e.g., the ratio of specific amplicons toside-products.

Assays of the present invention detect human parvovirus present in abiological sample (e.g., blood, serum, plasma, sputum, bronchiallavage). In one embodiment, the assay detected parvovirus DNA in plasmasamples that are from individual donors, or from a pooled collection ofdonor samples. To prepare plasma specimens, whole blood samples werecentrifuged using standard methods, and the plasma was stored at 4.deg.C or −20.deg. C before testing. To lyse viral particles in the specimen,a lysing reagent containing a detergent was mixed with the specimen torelease the parvovirus DNA from viral particles. Specimen processing maycombine viral lysis with purification of the viral target DNA byincluding a capture oligomer and immobilized oligomer in the lysingreagent. Then the method includes a target capture step in which theparvovirus DNA is hybridized specifically to the capture oligomer, whichis then hybridized to the immobilized oligomer, and the bound complex(i.e., immobilized oligomer, capture oligomer, and viral target DNA) issubstantially separated from other sample components. Washing the solidsupport with the bound parvovirus-containing complex washes residualsample components away. Thus, the viral target DNA is separated fromother sample components and concentrated in the bound complexes, withoutreleasing the bound parvovirus nucleic acid from the solid support.

Typical sample processing involved the following steps (described indetail in U.S. Pat. No. 6,110,678). Viral particles in body fluid (e.g.,0.5 ml of plasma) were lysed upon contact at 60.deg. C with targetcapture reagent (790 mM HEPES, 680 mM LiOH, 10% lithium lauryl sulfate(LLS), 230 mM succinate, at least one capture probe at 7 pm/ml, and 100μg/ml of poly-dT₁₄ bound to magnetic particles (SERADYN™, Indianapolis,Ind.)). Capture oligomers comprised a 5′ target-binding region sequence(e.g., SEQ ID NOs. 1, 2, 20, 21 and 53). Capture oligomers furthercomprised homopolymer or non-homopolymer 3′ tail sequence thathybridizes to the complementary oligomer attached to the solid support(e.g., an oligo-dT attached to a solid support and an oligo-dA tailportion of a capture oligomer). Other preferred embodiments of captureprobes are oligomers comprising a 5′ target-binding sequence of 27 to 33nucleotides in length that contains SEQ ID NO:41 and that furthercomprise an immobilized probe-binding region sequence at its 3′ end.Still other preferred embodiments of capture probes comprise a 5′target-binding sequence that is configured to bind specifically to aregion of a human parvovirus nucleic acid, said region corresponding toresidues 2505 to 2532 of SEQ ID NO:90 (SEQ ID NO:22) and that furthercomprise an immobilized-probe binding region sequence at its 3′ end.Another preferred embodiment comprises a 5′ target-binding sequence thatis configured to bind specifically to a region within a target sequenceof a human parvovirus nucleic acid, said region corresponding toresidues 2065 to 2101 of GenBank Accession No. DQ225149.1 gi:77994407(SEQ ID NO:29) and further comprises a 3′ immobilized-probe bindingregion. Target capture hybridization occurs in this reaction mixture byincubating the mixture at a first temperature (60.deg. C), allowing thecapture oligomer to bind specifically to its complementary targetsequence in a parvovirus DNA. Then, the mixture was cooled to 40.deg. Cor lower (e.g., room temperature) to allow the 3′ tail of the captureoligomer to hybridize to its complementary oligomer on the particle.Following the second hybridization, the mixture is treated to separatethe solid support with its bound complex of nucleic acids from the othersample components, e.g., by using gravitational, centrifugal, ormagnetic separation. Generally, separation employed a rack containing amagnet to pull the magnetic particles with bound nucleic acid complexesto the side of the tube. Then the supernatant was removed and the boundcomplexes on the particles were washed with 1 ml of a washing buffer (10mM HEPES, 6.5 mM NaOH, 1 mM EDTA, 0.3% (v/v) absolute ethanol, 0.02%(w/v) methyl paraben, 0.01% (w/v) propyl paraben, 150 mM NaCl, 0.1%sodium dodecyl sulfate (SDS), pH 7.5) by suspending the magneticparticles in washing buffer, separating particles to the tube side, andremoving the supernatant.

Following sample preparation, amplification of the parvovirus DNA targetwas achieved by using amplification oligomers that define the 5′ and 3′ends of the region amplified by in vitro enzyme-mediated nucleic acidsynthesis to generate an amplicon. One embodiment uses atranscription-mediated amplification (TMA) method, substantially asdescribed in U.S. Pat. Nos. 5,399,491 and 5,554,516, which is asubstantially isothermal system that produces a large number ofamplification products (RNA transcripts) that can be detected. Preferredembodiments of the method used mixtures of amplification oligomers inwhich at least one promoter primer is combined with at least one primer.

A preferred embodiment of amplification oligomer combinations comprisesa primer oligomer member and a promoter-based oligomer member.Preferably, a promoter-based amplification oligomer is a promoter primercomprising a 5′ RNA polymerase promoter sequence and a 3′ target bindingsequence. RNA polymerase promoter sequences are known in the art toinclude, but not be limited to, sp6 RNA polymerase promoter sequences,T3 RNA polymerase promoter sequences and T7 RNA polymerase promotersequences. In the preferred embodiments, a promoter primer comprises a5′ T7 RNA polymerase promoter sequence and a 3′ target binding sequence.Most preferably, the 5′ T7 RNA polymerase promoter sequence is SEQ IDNO:19.

In one preferred embodiment, the 3′ target binding sequence of apromoter-based amplification oligomer is from about 10 to about 40nucleobases in length and comprises a nucleic acid sequence that isconfigured to specifically hybridize to a region within a targetsequence of a human parvovirus nucleic acid, wherein said region is fromresidue 2428 to residue 2438 of GenBank Accession Number DQ225149.1,gi:77994407. GenBank Accession Number DQ225149.1, gi:77994407 isreferenced herein as SEQ ID NO:90, and the region corresponding to fromresidue 2428 to residue 2438 thereof is referenced herein as SEQ IDNO:83. Promoter-based oligomer members of the current invention aredescribed herein. These descriptions need not be repeated here. Someparticularly preferred promoter primers are SEQ ID NOS:56, 76, 66, 23,81, 72 and 61. Other preferred promoter primers comprise an internal tagsequence, which is flanked on its 5′ end by a promoter sequence, and onits 3′ end by a target binding sequence. Internal tag sequences are alsoreferred to herein as insert sequences. An internal tag sequence is anynucleic acid sequence that preferably does not stably hybridize with thetarget nucleic acid or interfere with the target binding sequencehybridizing with the target nucleic acid. Moreover, an internal tagsequence is preferably of a sufficient length and composition such thatonce incorporated into an amplification product, a tag-specificamplification oligomer can be used to participate in subsequent roundsfor generating amplification product. One preferred tag sequence is fromabout 10 nucleotides in length to about 50 nucleotides in length.Another preferred tag sequence is about 12 nucleotides in length. Afurther preferred tag sequence is about 12 nucleotides in length andcomprises the nucleotide sequence 5′-CCTACGATGCAT-3′ (SEQ ID NO:94). Apreferred tag sequence is SEQ ID NO:94. Another preferred tag sequenceis about 20 nucleotides in length. A further preferred tag sequence isabout 20 nucleotides in length and comprises the nucleotide sequence5′-GTCATATGCGACGATCTCAG-3′ (SEQ ID NO:95). A preferred tag sequence isSEQ ID NO:95. Particularly preferred promoter primers comprising a 3′target binding sequence, and internal tag sequence and a 5′ promotersequence are SEQ ID NOS:63, 73, 67, 68, 78, 82 and 58. Ordinarilyskilled artisans will recognize that the design of a tag sequence andits incorporation into an amplification oligomer of the currentinvention can follow any of a number of design strategies, while stillfalling within the objectives and advantages described herein. Moreover,it is recognized that insert sequences can be included with any of thepromoter-based oligomer members of the current invention.

In a preferred embodiment, the amplification oligomer combinationcomprises at least one primer amplification oligomer member. Preferredprimer amplification oligomers have a length that is from about 10nucleobases to about 50 nucleobases, and have a nucleotide compositionconfigured to specifically hybridize with human parvovirus types 1, 2and 3 to generate a detectable amplification product when used in anamplification reaction of the current invention. One preferred primeroligomer is from about 10 to about 50 nucleobases in length and has atarget binding sequence that is configured to specifically hybridize allor a portion of a region of a target sequence of a human parvovirusnucleic acid, wherein said region corresponds to from residue 2304 toresidue 2332 of GenBank Accession Number DQ225149.1, gi:77994407 (SEQ IDNO:96). Primer oligomer members of the current invention are describedherein. These descriptions need not be repeated here. Particularlypreferred primer oligomer members are selected from the group consistingof SEQ ID NOS:18, SEQ ID NO:48; SEQ ID NO:50 and SEQ ID NO:96. Oneparticularly preferred primer oligomer member comprises a target-bindingsequence that is SEQ ID NO:50. Another particularly preferred primeroligomer member comprises a target binding sequence that is SEQ IDNO:48. Other preferred primer oligomer members comprise a 5′ tagsequence. An 5′ tag sequence is any nucleic acid sequence thatpreferably does not stably hybridize with the target nucleic acid orinterfere with the target binding sequence hybridizing with the targetnucleic acid. Moreover, a 5′ tag sequence is preferably of a sufficientlength and composition such that once incorporated into an amplificationproduct, a tag-specific amplification oligomer can be used toparticipate in subsequent rounds for generating amplification product.One preferred 5′ tag sequence is from about 10 nucleotides in length toabout 50 nucleotides in length. Another preferred tag sequence is about12 nucleotides in length. A further preferred tag sequence is about 12nucleotides in length and comprises the nucleotide sequence5′-CCTACGATGCAT-3′ (SEQ ID NO:94). A preferred tag sequence is SEQ IDNO:94. Another preferred tag sequence is about 20 nucleotides in length.A further preferred tag sequence is about 20 nucleotides in length andcomprises the nucleotide sequence 5′-GTCATATGCGACGATCTCAG-3′ (SEQ IDNO:95). A preferred tag sequence is SEQ ID NO:95. Particularly preferredprimer oligomer members with a 5′ tag sequence are SEQ ID NOS:47 & 49.Ordinarily skilled artisans will recognize that the design of a tagsequence and its incorporation into an amplification oligomer of thecurrent invention can follow any of a number of design strategies, whilestill falling within the objectives and advantages described herein.Moreover, it is recognized that 5′ tag sequences can be included withany of the primer oligomer members of the current invention.

Amplifying the target nucleic acid by transcription-mediatedamplification produces many strands of nucleic acid from a single copyof target nucleic acid, thus permitting detection of the target bydetecting probes that hybridize to the sequences of the amplificationproduct. Generally, the reaction mixture includes the target nucleicacid and at least two amplification oligomers comprising at least oneprimers, at least one promoter primer, reverse transcriptase and RNApolymerase activities, nucleic acid synthesis substrates(deoxyribonucleoside triphosphates and ribonucleoside triphosphates) andappropriate salts and buffers in solution to produce multiple RNAtranscripts from a nucleic acid template. Briefly, a promoter-primerhybridizes specifically to a portion of the target sequence. Reversetranscriptase that includes RNase H activity creates a first strand cDNAby 3′ extension of the promoter-primer. The cDNA is hybridized with aprimer downstream from the promoter primer and a new DNA strand issynthesized from the 3′ end of the primer using the reversetranscriptase to create a dsDNA having a functional promoter sequence atone end. RNA polymerase binds to dsDNA at the promoter sequence andtranscribes multiple transcripts or amplicons. These amplicons arefurther used in the amplification process, serving as a template for anew round of replication, to ultimately generate large amounts ofsingle-stranded amplified nucleic acid from the initial target sequence(e.g., 100 to 3,000 copies of RNA synthesized from a single template).The process uses substantially constant reaction conditions (i.e.,substantially isothermal). A typical 100 μl amplification reaction uses75 μl of an amplification reagent mixture (11.6 mM Tris Base, 15.0 mMTris-HCl, 22.7 mM MgCl₂, 23.3 mM KCl, 3.33% glycerol, 0.05 mM Zn-acetate(dihydrate), 0.665 mM each of dATP, dCTP, dGTP, and dTTP, 5.32 mM eachof ATP, CTP, GTP, and UTP, pH 7) and 25 μl of an enzyme reagent mixture(700 U of T7 RNA polymerase, 1400 U of reverse transcriptase fromMoloney Murine Leukemia Virus (MMLV-RT), 16 mM HEPES (free acid,dihydrate), 70 mM N-acety-L-cysteine, 3 mM EDTA, 0.05% (w/v) Na-azide,20 mM Tris base, 50 mM KCl, 20% (v/v) anhydrous glycerol, 10% (v/v)TRITON® X-102, and 150 mM trehalose (dihydrate), pH 7), preferably mixedwith the captured target nucleic acid retained on the solid particles.For the enzymatic activities, 1 U of T7 RNA polymerase incorporates 1nmol of ATP into RNA in 1 hr at 37.deg. C using a DNA templatecontaining a T7 promoter, and 1 U of MMLV-RT incorporates 1 nmol of dTTPinto DNA in 10 mM at 37.deg. C using 200-400 μmol oligo dT-primedpoly(A) as a template.

In one preferred embodiment, a TMA reaction is performed using acombination of amplification oligomers, wherein said combinationcomprises at least one promoter primer oligomer member and at least oneprimer oligomer member, and wherein said combination is configured togenerate amplification products for the detection of human parvovirustypes 1, 2 and 3. In an aspect of this embodiment, the amplificationoligomer combination comprises at least one promoter primer oligomermember comprising a 5′ promoter sequence, an internal tag sequence and a3′ target binding sequence. In an aspect of this embodiment, theamplification oligomer combination comprises at least one promoterprimer oligomer member comprising a 5′ promoter sequence, an internaltag sequence and a 3′ target binding sequence, and also comprises atleast one promoter primer oligomer member comprising a 5′ promotersequence and a 3′ target binding sequence. In an aspect of thisembodiment, the amplification oligomer combination comprises at leastone primer oligomer member comprising a 5′ tag sequence and a 3′ targetbinding sequence. In an aspect of this embodiment, the amplificationoligomer combination comprises at least one primer oligomer membercomprising a 5′ tag sequence and a 3′ target binding sequence, and alsocomprises at least one primer oligomer member comprising a 3′ targetbinding sequence.

In another preferred embodiment, the TMA reaction is performed with anamplification oligomer combination comprising at least one promoterprimer oligomer member and at least one primer oligomer member, whereinconfigured to generate amplification products for the detection of humanparvovirus types 1, 2 and 3, and wherein said amplification oligomercombination is configured to generate from GenBank Accession NoDQ225149.1 gi:77994407 an amplicon that is about 100 nucleobases inlength to about 225 nucleobases in length and comprises a targetspecific sequence that contains SEQ ID NO:39. As is discussed herein,and thus will not be repeated in detail here, amplicons generated usingthe amplification oligomer combinations of the current inventionamplicons comprise, for example, target sequences containing SEQ IDNOS:25, 26, 39, 86, 97, 88, 89, 98, 99, 100 and combinations thereof.Ordinarily skilled artisans will recognize that the design of anamplification reaction using an amplification oligomer combination caninclude primer pairs, promoter-based amplification oligomer pairs or oneor more primer members combined with one or more promoter-basedamplification oligomer members, and can be any type of amplificationreaction, while still falling within the objectives and advantagesdescribed herein. Further, ordinarily skilled artisans will recognizethat an amplification oligomer combination can be configured to generatefrom SEQ ID NO:90, amplicons that are larger or smaller than what isillustrated here, and such amplicons will fall within the objectives andadvantages described herein.

Following amplification, the amplified sequences generated from theparvovirus DNA are detected, preferably by hybridization with at leastone labeled nucleic acid probe that hybridizes specifically to a portionof the amplified sequence. Probe embodiments include those having aT_(m) in the range of about 80.deg. C to about 85.deg. C. Some preferredprobe embodiments include oligomers having a nucleotide length of fromabout 15 to about 40 nucleotides and a nucleic acid sequence that isDNA, RNA or a combination there of and is configured to specificallyhybridize with all or a portion of a region of a target sequence of ahuman parvovirus nucleic acid or amplified nucleic acid, said regionbeing from residue 2376 to residue 2409 of GenBank Accession NumberDQ225149.1, gi:77994407 (SEQ ID NO:33). Detection probe oligomers of thecurrent invention are described herein. These descriptions need not berepeated here. Particularly preferred probe embodiments includeoligomers selected from the group consisting of SEQ ID NO:28, SEQ IDNO:30, SEQ ID NO:31, SEQ ID NO:32, SEQ ID NO:42, SEQ ID NO:43, SEQ IDNO:44 and SEQ ID NO46. Preferably, detection oligomers of the currentinvention further comprise one or more LNA residues. Detection of theprobe is preferably accomplished by detecting a label that can bedetected in a homogeneous reaction. Therefore, some preferredembodiments further comprise probes labeled with an acridinium ester(AE) compound using well-known methods that allow homogeneous detection(e.g., labels and detection methods are described in detail in U.S. Pat.No. 5,283,174 to Arnold, Jr., et al., U.S. Pat. No. 5,656,207 toWoodhead et al., and 5,658,737 to Nelson et al.). A chemiluminescent AEcompound is attached to the probe sequence via a linker compound(substantially as described in U.S. Pat. Nos. 5,585,481 and 5,639,604 toArnold, Jr., et al., e.g., see column 10, line 6 to column 11, line 3,and Example 8). In one embodiment, the labeled probe oligomer has atleast one 2′-O-methoxy linkage in the nucleic acid backbone. In atypical detection step, the probe reagent included 100 mM succinate, 2%(w/v) LLS, 230 mM LiOH (monohydrate), 15 mM 2,2′-dithiodipyridine(ALDRITHIOL-2), 1.2 M LiCl, 20 mM EDTA, 20 mM EGTA, 3% (v/v) absoluteethanol, brought to about pH 4.7 with LiOH, and the selection reagentused for hydrolyzing the label on unbound probe included 600 mM boricacid, 182 mM NaOH, 1% (v/v) TRITON® X-100. The signal was detected asrelative light units (RLU) using a luminometer (e.g., LEADER™ 450HC+,Gen-Probe Incorporated, San Diego, Calif.).

To select DNA sequences appropriate for use as capture oligomers,amplification oligomers and detection probes, known parvovirus types 1,2 and 3 DNA sequences, including partial or complementary sequences,available from publicly accessible databases (e.g., GenBank) werealigned by matching regions of the same or similar sequences andcompared using well known molecular biology techniques. Althoughsequence comparisons may be facilitated by use of algorithms, thoseskilled in the art can readily perform such comparisons manually andvisually. Generally, portions of sequences that contain relatively fewvariants between the compared sequences were chosen as a basis fordesigning synthetic oligomers for use in the present invention. Otherconsiderations in designing oligomers included the relative GC content(which affects T_(m)) and the relative absence of predicted secondarystructure (which potentially form intramolecular hybrids) within asequence, as determined by using well-known methods.

In one embodiment, the assay is carried out in a single tube using a 0.5to 1 ml sample of body fluid (e.g., plasma) to detect target parvovirusDNA at a sensitivity of about 100 to 500 copies/ml of target DNA perreaction. In other embodiments, the assay detected higher numbers oftarget parvovirus DNA in the sample, which may be a pooled sample ofindividual samples.

Unless defined otherwise, all scientific and technical terms used hereinhave the same meaning as commonly understood by those skilled in therelevant art. General definitions of many of the terms used herein areprovided in Dictionary of Microbiology and Molecular Biology, 2nd ed.(Singleton et al., 1994, John Wiley & Sons, New York, N.Y.), The HarperCollins Dictionary of Biology (Hale & Marham, 1991, Harper Perennial,New York, N.Y.), and Taber's Cyclopedic Medical Dictionary, 17th ed.(F.A. Davis Co., Philadelphia, Pa., 1993). Unless mentioned otherwise,the techniques employed or contemplated herein are standardmethodologies well known to one of ordinary skill in the art. Thefollowing examples illustrate some of the preferred embodiments of theinvention and are provided for illustration only.

Example 1: Target Capture of Parvovirus DNA

Capture probes were synthesized by standard in vitro DNA synthesisreactions having sequences of SEQ ID NO:1, SEQ ID NO:2, SEQ ID NO:20,SEQ ID NO:21 and SEQ ID NO: 52, all having 3′ dA₃₀ tail portions or a 3′dT₃, dA₃₀ tail portions. In a first experiment, SEQ ID NOS:1 and 2 wereseparately assayed for capture of a human parvovirus from plasma. Usingthe target capture methods described above, the capture oligomers weremixed with human plasma samples obtained from uninfected donors, eachsample was spiked with a known number of copies of live parvovirus B19(2,000, 1,000, 500 or 0 in the negative control). The virions were lysedby mixing the plasma sample (generally 0.5 ml) with an equal volume oftarget capture reagent containing each of the capture probes separately(3.5 pmol per reaction). Following capture by hybridization at about60.deg. C for about 20 min and then at 18-25.deg. C for about 10-20 min,the magnetic particles with attached hybridization complexes were washedtwice as described above. The parvovirus target sequence in thecomplexes retained on the particles was amplified in a TMA reactionperformed substantially as described herein and in Example 2, and theamplified target sequences were detected by hybridization with anAE-labeled probe (SEQ ID NO:17). The results (RLU detected from bounddetection probe) are shown in Table 1. These results (RLU of about1.5×10.sup.6) show that both capture probes specifically bind to andeffectively capture parvovirus DNA from a sample compared to thenegative control (RLU about 2×10.sup.4).

TABLE 1 Detection of labeled probe (RLU) bound to parvovirus DNAfollowing target capture. B19 copies per A₃₀ Capture Probe A₃₀ CaptureProbe reaction SEQ NO: 1 SEQ NO: 2 2,000 1.56 × 10.sup.6 1.61 × 10.sup.61,000 1.42 × 10.sup.6 1.53 × 10.sup.6 500 1.58 × 10.sup.6 1.59 ×10.sup.6 0 1.98 × 10.sup.4 2.44 × 10.sup.4

In a second target assay, SEQ ID NOS:1, 20 and 21 target captureoligomers were assayed separately and in combination for capture ofhuman parvovirus type 1 from plasma. Reactions included each of SEQ IDNOS 1, 20 and 21 individually, and in the various possible combinations(SEQ ID NOS 1 and 20, SEQ ID NOS 1 and 21, SEQ ID NOS 20 and 21, and SEQID NOS 1, 20 and 21). Plasma sample containing parvovirus type 1 weremixed with a lysing reagent and a capture reagent containing one or moreof the capture oligomers at 3.5 pmol each per reaction and wereincubated and hybridized as discussed above. Following separation andwash the attached hybridization complexes were incubated in a TMAamplification mixture containing 15 pmol per reaction of each of SEQ IDNO:23 and SEQ ID NO:13, and the appropriate salts, nucleotides andenzymes. Detection was performed using SEQ ID NO:17 labeled with2-methyl-AE between nt 7 and nt 8 and the chemiluminescent signal wasdetected (RLU) as described in detail previously (U.S. Pat. Nos.5,283,174, 5,656,207, and 5,658,737).

The tested human plasma samples contained either no parvovirus (negativesamples) or 1,000 copies per reaction of parvovirus (positive samples),which were prepared by dilution from a stock sample of infected plasma(from the American Red Cross) that had been titrated by comparison witha standardized sample (IS 99/800 from National Institute for BiologicalStandards and Control, “NIBSC,” Hertfordshire, England). Ten replicatesamples were tested for each of the conditions. The detected results(RLU mean±standard deviation) are shown in Table 2.

TABLE 2 Results of Assays Performed Using Different Capture Oligomers.Capture Oligomers Negative Samples Positive Samples SEQ ID NO: 1 2,461 ±1,252 4,067,173 ± 163,492 SEQ ID NO: 20 2,137 ± 360   3,893,205 ±477,513 SEQ ID NO: 21 4,774 ± 6,970 3,954,416 ± 468,324 SEQ ID NOS: 1and 20 5,285 ± 4,911 4,078,141 ± 269,686 SEQ ID NO: 1 and 21 2,560 ±1,002 4,093,581 ± 271,294 SEQ ID NO: 20 and 21 2,164 ± 301   4,000,996 ±361,454 SEQ ID NO: 1, 20 and 21 4,291 ± 4,919 3,994,533 ± 116,348

The target capture oligomer combinations were tested again, this timethe plasma samples contained no parvovirus (negative samples) or varyingamounts of parvovirus (1,000, 500, 250, 100 and 50 copies per reaction),prepared by dilution from the stock sample described above. For each ofthe conditions, five replicate samples were tested for those containing1,000 and 0 copies of parvovirus B19, and ten replicate samples weretested for all the others. The detected results (RLU mean±standarddeviation) are shown below in Table 3. For all of the negative controls(0 copies per reaction), the detected background was in the range of2,277±215 to 4,724±3,889 RLU.

TABLE 3 Sensitivity of Assays Performed Using Different CaptureOligomers SEQ ID Copies of Parvovirus Per Reaction NOS 1,000 500 250 10050 1 4.04 × 10.sup.6 ± 3.80 × 10.sup.6 ± 3.55 × 10.sup.6 ± 1.89 ×10.sup.6 ± 8.04 × 10.sup.5 ± 4.18 × 10.sup.5 5.01 × 10.sup.5 8.04 ×10.sup.5 1.55 × 10.sup.6 1.34 × 10.sup.6 20 4.00 × 10.sup.6 ± 3.89 ×10.sup.6 ± 2.78 × 10.sup.6 ± 2.06 × 10.sup.6 ± 1.85 × 10.sup.6 ± 3.60 ×10.sup.5 5.63 × 10.sup.5 1.22 × 10.sup.5 1.59 × 10.sup.6 1.73 × 10.sup.521 4.27 × 10.sup.6 ± 4.00 × 10.sup.6 ± 3.25 × 10.sup.6 ± 1.26 × 10.sup.6± 7.13 × 10.sup.5 ± 5.85 × 10.sup.4 3.22 × 10.sup.5 1.24 × 10.sup.6 1.05× 10.sup.6 1.28 × 10.sup.6  1 & 20 4.14 × 10.sup.6 ± 3.51 × 10.sup.6 ±3.57 × 10.sup.6 ± 2.10 × 10.sup.6 ± 1.13 × 10.sup.6 ± 1.71 × 10.sup.61.34 × 10.sup.5 9.30 × 10.sup.5 1.66 × 10.sup.6 1.52 × 10.sup.6  1 & 214.28 × 10.sup.6 ± 3.78 × 10.sup.6 ± 3.23 × 10.sup.6 ± 1.60 × 10.sup.6 ±1.44 × 10.sup.6 ± 8.45 × 10.sup.4 1.16 × 10.sup.6 1.08 × 10.sup.6 1.33 ×10.sup.6 1.60 × 10.sup.6 20 & 21 4.15 × 10.sup.6 ± 4.26 × 10.sup.6 ±2.68 × 10.sup.6 ± 1.55 × 10.sup.6 ± 1.06 × 10.sup.6 ± 2.10 × 10.sup.51.49 × 10.sup.5 1.76 × 10.sup.6 1.69 × 10.sup.6 1.28 × 10.sup.6 1, 20 &4.24 × 10.sup.6 ± 4.35 × 10.sup.6 ± 2.56 × 10.sup.6 ± 2,529,303 ± 9.62 ×10.sup.5 ± 21 1.30 × 10.sup.5 1.09 × 10.sup.5 1.59 × 10.sup.6 1,652,5371.46 × 10.sup.6

The results of these experiments show that when the assay was performedwith any of these three capture oligomers, alone or in a mixture, eachformat detected the presence of parvovirus B19. The assays resulted inpositive signals for all samples that contained 250 to 1,000 copies/ml,for 80 to 90% of samples that contained 100 copies/ml, and for 50 to 70%of samples that contained 50 copies/ml.

Example 2: Detection of Parvovirus in an Amplification Assay That UsesTarget Capture

In this example, the target capture assay was performed substantially asdescribed in Example 1 using SEQ ID NO:1 or SEQ ID NO:2. Amplificationand detection steps were performed substantially as follows. A knownamount of parvovirus type 1 target nucleic acid (denatured ssDNA at 500,250, 100, 50 and 0 copies per reaction tube) was amplified in a TMAreaction using reagents (75 μl per reaction) as described abovecontaining a promoter primer of SEQ ID NO:3 with a primer of SEQ IDNO:13 or a promoter primer of SEQ ID NO:5 with a primer of SEQ ID NO:13(7.5 pmol each amplification oligomer member per reaction). The mixturewas incubated 10 min at 60.deg. C, then 10 min at 42.deg. C. Then 25 μlof enzyme reagent was added and the tubes were mixed by hand and thenincubated 60 min at 42.deg. C. Following amplification the samples wereincubated at 60.deg. C and 100 μl of probe reagent containing probe ofSEQ ID NO:17 was added. The mixture was incubated 20 min at 60.deg. Cand then 300 μl of selection reagent was added, mixed, and incubated 10min at 60.deg. C and 10 min at room temperature before detecting thesignal (RLU) as described above. The results shown in Table 4 are for anaverage of 5 samples for each of the conditions tested. These resultsshow that the sensitivity of the assay is about 250 copies of targetparvovirus type 1 DNA in the sample or better (i.e., capable ofdetecting 100 copies per sample). The primer set of SEQ ID NO:3 plus SEQID NO:13 had sensitivity of better than 250 copies of virus in capturefrom plasma, as well has stable, reproducible signal with 100 copiessensitivity in an amplification and detection assay.

TABLE 4 Detected signal (RLU) for target capture plus amplificationassays. Oligomers SEQ ID NOS: Copies of Parvovirus Type 1 Capture Amp500 250 100 0 1 3 & 13 1.30 × 10.sup.6 1.30 × 10.sup.6 9.86 × 3.30 ×10.sup.5 10.sup.4 5 & 13 2.37 × 10.sup.6 2.91 × 10.sup.5 2.52 × 4.66 ×10.sup.5 10.sup.4 2 3 & 13 9.65 × 10.sup.5 8.88 × 10.sup.5 7.85 × 1.15 ×10.sup.5 10.sup.5 5 & 13 2.06 × 10.sup.5 1.03 × 10.sup.5 4.14 × 3.51 ×10.sup.4 10.sup.3

Example 3: Amplification of Parvovirus Sequences Using VariousAmplification Oligomers

This example shows that different combinations of amplificationoligomers serving as primers can efficiently amplify the targetsequences in parvovirus DNA. The target sequences were amplified byusing a combination of primers that had the target specific sequence ofSEQ ID NO:24, SEQ ID NO:4 and SEQ ID NO:13. SEQ ID NOS:24 and 4 furthercomprised the promoter sequence SEQ ID NO:19. Samples were prepared bymixing human plasma that does not contain parvovirus (negative control)with aliquots of parvovirus to produce samples containing 10,000, 5,000,1,000, 500, 250, 100, 50, and 25 copies of parvovirus per ml. As apositive control, standard samples containing 1,000 copies of parvovirusper ml were also assayed. The samples were first mixed with a targetcapture oligomer (SEQ ID NO:1) which was allowed to hybridize to theparvovirus DNA, and then the hybridization complex containing theparvovirus DNA was separated from the sample by hybridizing it to anoligomer attached to a magnetic bead, substantially as describedpreviously (U.S. Pat. No. 6,110,678).

The amplification assays were performed using the TMA systemsubstantially as described above. The amplification reaction contained15 pmol each of the promoter primer of SEQ ID NO:23 and the primer ofSEQ ID NO:13, or 15 pmol each of the promoter primer of SEQ ID NO:3 andthe primer of SEQ ID NO:13. Following the one-hour amplificationreaction, the mixtures were hybridized with a detection probe of SEQ IDNO:17 labeled with a chemiluminescent compound between nt 7 and 8 (using5.5×10.sup.9 RLU per reaction), and the relative light unit (RLU)signals were detected as described above. For the positive and negativecontrols, 5 replicate samples were tested. For the experimental samples,10 replicates were tested for each condition. The results of theseassays (RLU mean±standard deviation) are shown in Table 5.

TABLE 5 Assay Results Obtained Using Various Amplification OligomersParvovirus B19 SEQ ID NO: 13 and SEQ ID NO: 13 and copies/ml SEQ ID NO:23 Primers SEQ ID NO: 3 Primers 1,000 3.87 × 10.sup.6 ± 2.53 × 10.sup.6± (positive control) 1.89 × 10.sup.5 7.94 × 10.sup.5 10,000 4.20 ×10.sup.6 ± 4.03 × 10.sup.6 ± 8.27 × 10.sup.4 7.29 × 10.sup.5 5,000 4.07× 10.sup.6 ± 3.97 × 10.sup.6 ± 2.73 × 10.sup.5 1.15 × 10.sup.5 1,0003.80 × 10.sup.6 ± 2.77 × 10.sup.6 ± 7.38 × 10.sup.5 6.63 × 10.sup.5 5003.17 × 10.sup.6 ± 1.82 × 10.sup.6 ± 1.09 × 10.sup.6 1.13 × 10.sup.6 2502.90 × 10.sup.6 ± 1.07 × 10.sup.6 ± 7.57 × 10.sup.5 5.83 × 10.sup.5 1001.73 × 10.sup.6 ± 3.79 × 10.sup.5 ± 1.54 × 10.sup.6 4.73 × 10.sup.5 501.74 × 10.sup.6 ± 2.34 × 10.sup.5 ± 1.74 × 10.sup.4 5.96 × 10.sup.5 252.20 × 10.sup.5 ± 2.52 × 10.sup.5 ± 5.66 × 10.sup.5 7.83 × 10.sup.5 0(negative control) 2.73 × 10.sup.3 ± 3.57 × 10.sup.3 ± 5.12 × 10.sup.22.37 × 10.sup.3

The results show that both combinations of oligomers used as primersperformed substantially equally in the assay to amplify parvovirussequences. In both assay formats, positive signals were detected for allof the samples containing 250 or more copies of parvovirus B19, andpositive signals were detected for 70 to 80% of the samples containing100 copies.

Example 4: Parvovirus Detection Assays Performed With Various DetectionProbes

In this example, parvovirus was assayed by using substantially themethod described in Example 2. Briefly, samples were prepared usinghuman plasma that contains no parvovirus (negative control), by addingknown amounts of parvovirus (to achieve final concentrations of 10,000,5,000, 1,000, 500, 250, 100, 50, and 25 copies per ml). Previouslytested known samples containing 1,000 copies of parvovirus per ml wereincluded as positive controls. Samples were assayed by first capturingthe parvovirus DNA from a 1 ml sample by hybridization to acomplementary oligomer (SEQ ID NO:1) which was then hybridized via its3′ poly(A) tail to a complementary poly(T)-oligomer attached to magneticbeads using procedures substantially as described. Then, a targetportion of the parvovirus genomic sequence was amplified in a one-hourTMA reaction using a promoter primer of SEQ ID NO:23 (comprising thetarget-specific sequence of SEQ ID NO:24 and a T7 RNA polymerasepromoter sequence of SEQ ID NO:19) and a primer of SEQ ID NO:13. Theamplification products were detected by using detection probes labeledwith 2-methyl-AE in a reaction to detect relative light units (RLU) asdescribed in detail previously (U.S. Pat. Nos. 5,585,481 and 5,639,604).The detection probes were synthesized by using standard chemical methodsto produce oligomers with a 2′-O-methoxy backbone and having thenucleotide sequences of SEQ ID NO:17 (label between nt 7 and 8), SEQ IDNO:27 (label between nt 5 and 6), and SEQ ID NO:28 (label between nt 9and 10). Two separate sets of assays were performed, one in which thedetection results were obtained by using SEQ ID NOS:17 and 27, andanother in which detection results were obtained by using SEQ ID NOS:17and 28 (using 1×10.sup.6 RLU per reaction in both sets of assays). Tenreplicate samples were assayed for each of the experimental conditions,and five replicate samples were assayed for the positive (1,000 copies)and negative (0 copies) controls and the NIBSC standard (1,000 genomeequivalents/ml). The results of these tests (detected RLU mean±standarddeviation) are shown in Table 6.

TABLE 6 Detection of Amplified Parvovirus Target Sequences Using VariousDetection Probes Parvovirus SEQ ID NO: 17 SEQ ID NO: 27 SEQ ID NO: 28copies/ml Probe Probe Probe 1,000 273,238 ± 8,370  232,836 ± 7,843  —(positive 269,226 ± 9,517  — 237,152 ± 7,482  control) 10,000 282,473 ±6,037  258,127 ± 16,557  — 288,209 ± 5,299  — 242,686 ± 13,025  5,000283,015 ± 3,716  245,047 ± 5,292  — 282,135 ± 14,676  — 238,992 ± 3,790 1,000 263,795 ± 22,793  241,110 ± 7,211  — 261,161 ± 13,038  — 236,014 ±6,581  500 224,858 ± 83,219  216,921 ± 44,803  — 228,023 ± 50,281  —209,931 ± 49,130  250 167,216 ± 80,594  138,291 ± 53,137  — 158,861 ±100,765 — 144,024 ± 75,550  100 84,296 ± 77,843 79,058 ± 70,042 — 97,111± 97,430 — 56,746 ± 42,133 50 39,551 ± 49,759 30,533 ± 47,622 — 58,045 ±83,433 —  85,278 ± 101,652 25 16,403 ± 44,038 1,526 ± 1,700 — 41,375 ±72,116 — 57,283 ± 91,578 0 819 ± 232 518 ± 55  — (negative 786 ± 66  —512 ± 29  control) NIBSC 157,522 ± 67,888  97,318 ± 47,119 — Standard199,789 ± 68,636  — 191,507 ± 51,276 

The results showed that the three assay formats using differentdetection probes were substantially equivalent in their reactivity andsensitivity. That is, based on a positive signal of 30,000 or moredetected RLU, all three formats detected 100 copies or more ofparvovirus per ml of sample, and frequently detected fewer copies ofparvovirus (25 and/or 50 copies/ml).

Example 5: Detection of Amplified Parvovirus Sequences UsingCombinations of Detection Probes

This example tested the sensitivity of the assay using individualdetection probes or a mixture of two different detection probes. Themixture of detection probes contained equivalent amounts of probes ofSEQ ID NO:27 and SEQ ID NO:28. Assays compared the detection probemixture to use of either detection probe alone. The assays wereperformed substantially as described in Example 2, but using plasmasamples that contained no parvovirus (negative control), or contained500, 250, 100, 50, or 25 copies of parvovirus per ml; positive controlscontained 1,000 copies/ml. Samples (1 ml) were assayed by firstcapturing the parvovirus DNA in a hybridization complex on magneticparticles using an oligomer having SEQ ID NO:1 with a 3′ poly-A tail, asdescribed above. Then, the parvovirus target sequence was amplified byusing a one-hour TMA reaction that included a promoter primer of SEQ IDNO:23 and a primer of SEQ ID NO:13. The amplification products weredetected by using detection probes of either SEQ ID NO:27 or SEQ IDNO:28 individually, or a mixture of probes of SEQ ID NO:27 and SEQ IDNO:28. The probes were labeled with 2-methyl-AE (between nt 5 and 6 forSEQ ID NO:27, and nt 9/10 for SEQ ID NO:28) and used at an activity of1×10.sup.6 RLU per reaction for each probe. For the positive andnegative controls, five replicate samples were tested, whereas for eachof the other experimental conditions, twenty replicate samples weretested. The results (RLU mean±standard deviation) are shown below.

TABLE 7 Detection Results Using Labeled Probes Alone or in MixturesParvovirus SEQ ID NO: 27 and copies/ml SEQ ID NO: 27 SEQ ID NO: 28 SEQID NO: 28 1,000 464,906 ± 10,157  476,397 ± 8,369  828,543 ± 31,127 (positive control) 500 412,338 ± 95,435  457,938 ± 34,499  679,652 ±210,438 250 296,947 ± 179,021 397,804 ± 111,879 554,294 ± 272,640 100167,560 ± 153,175 262,557 ± 189,262 376,880 ± 254,070 50  95,581 ±145,780  70,364 ± 140,050  82,840 ± 145,301 0 1,046 ± 205   826 ± 1811,051 ± 116   (negative control)

The results show that both of the probes alone and in a mixture detectedparvovirus at 500 copies/ml in all of the assays performed. Samplescontaining fewer copies of parvovirus were also detected (90 to 100% for250 copies/ml, 75 to 85% for 100 copies/ml, and 30 to 50% for 50copies/ml). The sensitivities of the three assay formats weresubstantially equivalent.

Example 6: Parvovirus Detection Using Differently Labeled DetectionProbes

In this example, the amplified products produced using the methodsubstantially as described in Example 5 were detected using variousdetection probe oligomers. The detection probe oligomers varied from oneanother either in their nucleotide sequence or, for probe oligomers withthe same nucleotide sequence, at the position of label attachment to theoligomer. All of the probes were synthesized in vitro using standardchemical methods to produce an oligomer of specified sequence with a2′-O-methoxy backbone. Oligomers were labeled with 2-methyl-AE aspreviously described (U.S. Pat. Nos. 5,585,481 and 5,639,604) using alinker compound to attach the label compound to the oligomer and used atan activity of 1×10.sup.6 RLU per reaction. The label position on theoligomer is referred to by the adjacent nucleotide positions, e.g.,“12/13” means the linker and attached label are located between nt 12and nt 13 of the oligomer. Detection probe oligomers tested in theseexperiments are summarized in Table 8.

TABLE 8 Labeled Probes SEQ ID NO Nucleotide Sequence Label Positions 27GTCATGGACAGTTATCTGAC 7/8, 9/10, 12/13, and 13/14 28GTATTATCTAGTGAAGACTTAC 12/13 30 CTAGTGAAGACTTACACAAGC 5/6 and 13/14 31GTGAAGACTTACACAAGCCTG 9/10 and 10/11 32 GCAGTATTATCTAGTGAAGAC8/9 and 12/13 34 CAAAGTCATGGACAGTTATCTG7/8, 9/10, 11/12, 13/14, 16/17, and 17/18 36 CTGTTTGACTTAGTTGCTCG6/7, 7/8, 10/11, 11/12, 14/15, and 15/16 37 CTCTCCAGACTTATATAGTCATCAT7/8, 8/9, 9/10, 11/12, 12/13, 14/15, 16/17, 17/18, and 18/19

The results of assays that used these detection probes are shown below,reported as the average (mean) RLU detected. Each probe was tested infive replicate assays of human plasma samples that contained noparvovirus DNA (negative samples) and plasma that contained 1,000copies/ml of parvovirus (positive samples). The ratio of RLU detected inthe positive samples to RLU detected in the negative samples (detectionratio) was determined using the average RLU results for each probe.(Table 9).

TABLE 9 Results Obtained By Using Differently Labeled Probes SEQ ID NO.and Positive Samples Negative Samples Detection Label Position (meanRLU) (mean RLU) Ratio NO: 27, Label 7/8 287,160 409 702 NO: 27, Label9/10 419,399 610 687 NO: 27, Label 12/13 415,421 691 601 NO: 27, Label13/14 461,686 747 618 NO: 28, Label 12/13 383,934 864 444 NO: 30, Label5/6 432,460 874 495 NO: 30, Label 13/14 422,976 2,626 161 NO: 31, Label9/10 413,436 3,107 133 NO: 31, Label 10/11 545,659 3,398 160 NO: 32,Label 8/9 471,379 864 545 NO: 32, Label 12/13 445,970 473 943 NO: 34,Label 7/8 535,343 7,105 75 NO: 34, Label 9/10 473,386 1,044 453 NO: 34,Label 11/12 369,158 647 570 NO: 34, Label 13/14 364,239 823 442 NO: 34,Label 16/17 220,368 672 328 NO: 34, Label 17/18 373,932 950 393 NO: 36,Label 6/7 520,799 814 639 NO: 36, Label 7/8 482,847 792 609 NO: 36,Label 10/11 370,929 633 586 NO: 36, Label 11/12 343,754 757 454 NO: 36,Label 14/15 364,239 823 442 NO: 36, Label 15/16 382,139 1,016 376 NO:37, Label 7/8 336,293 61,020 5 NO: 37, Label 8/9 81,986 1,314 62 NO: 37,Label 9/10 516,495 57,853 9 NO: 37, Label 11/12 559,173 133,530 4 NO:37, Label 12/13 506,083 121,133 4 NO: 37, Label 14/15 593,889 54,116 5NO: 37, Label 16/17 439,755 94,380 4 NO: 37, Label 17/18 361,001 91,1634 NO: 37, Label 18/19 222,039 2,233 99

The results showed that a variety of different detection probes may beused to detect parvovirus sequences in the amplification product becauseall of the probes tested produced at least four-fold more signal thanthe negative controls. Preferred embodiments generally have a detectionratio of 10 or greater. More preferably, the detection ratio is 100 orgreater, and most preferably is in a range of 300 to 950. These resultsalso showed that, for the same nucleotide sequence, the position of thelabel on the oligomer may influence the detection signal produced.

Example 7: Amplification and Detection Oligomers for Detecting HumanParvovirus Genotypes 1, 2 and 3

The object of this example was to amplify and detect human parvovirusgenotypes 1, 2 and 3. Parvovirus nucleic acid sequences for genotypes 1,2 and 3 were obtained from GenBank and were aligned using the Clustal Wmultiple sequence alignment algorithm. In a first amplification anddetection assay, human parvovirus types 1-3 synthetic target nucleicacids were synthesized, (SEQ ID NO:91, SEQ ID NO:92 and SEQ ID NO:93,respectively). Twenty-five amplification oligomer combinations weredesigned and tested in an amplification and detection assay against 0,10 or 1000 copies per reaction of these three synthetic targets.Amplification oligomer combinations included one or more of: a primermember (SEQ ID NOS:48 & 50); a tagged primer member (SEQ ID NOS:47 &49); a T7 promoter primer (SEQ ID NOS:24, 56, 61, 76 & 81); and a T7promoter primer with insert (SEQ ID NOS:58, 63, 68, 73 & 78). One ormore inosine residues were substituted into SEQ ID NOS:73, 76, 78 & 81.Each positive condition was tested in triplicate, unless otherwisenoted. Negative controls were run in duplicate. Reactive assays provideda signal to noise ratio of at least 10, calculated by dividing theaverage RLU value obtained from the reaction wells by the average RLUvalue obtained from the negative control wells. Systems providing alarge standard deviation of RLU values under like conditions wereconsidered to provide inconclusive results and are listed in the tableas “undefined.”

The combinations of amplification oligomers were prepared and eachspiked into a primerless amplification reagent. These combinations wereadded to the reaction wells. A TMA amplification reaction was performedas substantially described above and was followed by a detectionreaction. Detection of amplification product produced in the reactionwells, was achieved using a hybridization protection assay with SEQ IDNO:42 detection probe. Briefly, probe reagent was added to each reactionwell, the detection reaction was incubated at 62.deg. C for 15 minutes,selection reagent was added followed by a 10 minute and 62.deg. Cincubation and then a 10 minute room temp incubation. Detection resultswere obtained using a luminometer, RLUs were averaged and signal tonoise ratios were calculated. A summary of the results is reported inTable 10 as “R”=reactive, “NR”=non-reactive, “Undef.”=undefined, or “nottested.” Signal-to-noise ratios are presented as “SN=v” where v is thecalculated value, rounded to no decimal place.

TABLE 10 Detection Results Using Human Parvovirus Types 1, 2 and 3Amplification and Detection Oligomers Amp Oligo Combos SEQ ID NOSt1-1000 t1-10 t2-1000 t2-10 t3-1000 t3-10 47 & 61 NR NR NR NR NR NR (SN= 3) (SN = 1) (SN = 1) (SN = 0) (SN = 3) (SN = 0) 47 & 58 R NR NR NR RNR (SN = 437) (SN = 1) (SN = 4) (SN = 3) (SN = 990) (SN = 9) 47, 56 & 23undef. undef. undef. undef. undef. undef. 47, 63 & 68 R R R NR R NR (SN= 542) (SN = 157) (SN = 232) (SN = 1) (SN = 368) (SN = 1) 47, 76 & 81 RNR R NR R NR (SN = 266) (SN = 3) (SN = 271) (SN = 1) (SN = 264) (SN = 1)47, 73 & 78 R NR R R R R (SN = 1427) (SN = 1) (SN = 2041) (SN = 96) (SN= 1363) (SN = 1595) 48 & 61 NR NR NR NR NR NR (SN = 3) (SN = 1) (SN = 3)(SN = 1) (SN = 3) (SN = 1) 48 & 58 NR NR NR NR R NR (SN = 6) (SN = 1)(SN = 4) (SN = 1) (SN = 21) (SN = 1) 48, 56 & 23 undef. undef. undef.undef. undef. undef. 48, 63 & 68 R NR R NR R NR (SN = 385) (SN = 7) (SN= 47) (SN = 1) (SN = 68) (SN = 1) 48, 76 & 81 R R R NR R R (SN = 210)(SN = 27) (SN = 217) (SN = 1) (SN = 215) (SN = 11) 48, 73 & 78 R NR R NRR R (SN = 577) (SN = 3) (SN = 583) (SN = 3) (SN = 951) (SN = 68) 48, 56& 23 R not tested R not tested R not tested (re-test) (SN = 433) (SN =214) (SN = 300) 49 & 61 NR NR NR NR NR NR (SN = 3) (SN = 2) (SN = 2) (SN= 1) (SN = 9) (SN = 2) 49 & 58 NR NR NR NR NR NR (SN = 3) (SN = 1) (SN =2) (SN = 2) (SN = 3) (SN = 1) 49, 56 & 23 R undef. NR NR R NR (SN = 211)(SN = 4) (SN = 7) (SN = 290) (SN = 1) 49, 63 & 68 R NR R NR R NR (SN =338) (SN = 2) (SN = 69) (SN = 1) (SN = 120) (SN = 4) 49, 76 & 81 R NR RNR NR NR (SN = 112) (SN = 1) (SN = 117) (SN = 1) (SN = 9) (SN = 6) 49,73 & 78 R R R NR R NR (SN = 232) (SN = 26) (SN = 187) (SN = 2) (SN =374) (SN = 3) 50 & 61 NR NR NR NR NR NR (SN = 3) (SN = 1) (SN = 2) (SN= 1) (SN = 3) (SN = 1) 50 & 58 undef. undef. undef. undef. undef. undef.50, 56 & 23 R NR R NR R NR (SN = 516) (SN = 1) (SN = 85) (SN = 3) (SN =508) (SN = 2) 50, 63 & 68 R NR R NR R NR (SN = 208) (SN = 1) (SN = 61)(SN = 1) (SN = 36) (SN = 1) 50, 76 & 81 R NR R R R NR (SN = 219) (SN= 1) (SN = 215) (SN = 72) (SN = 219) (SN = 6) 50, 73 & 78 R NR R NR R R(SN = 823) (SN = 3) (SN = 1081) (SN = 1) (SN = 1525) (SN = 16) 50, 61 &78* R not tested R not tested R not tested (SN = 578) (SN = 921) (SN =1086) *five reaction wells tested

Sample wells providing RLU values at least 10-fold greater, andpreferably at least 500-fold greater, than those provided by theircorresponding negative control well are acceptable for a qualitativeassay. Thus, a variety of the amplification oligomer combinations inthis example detected the synthetic constructs representing parvovirustypes 1, 2 and 3 target regions (SEQ ID NOS:91-93). The addition of a 5′tag sequence to SEQ ID NO:48 improved this primer member's performancewhen used with SEQ ID NO:61 promoter primer, but not when used with theSEQ ID NO:58 promoter primer. The use of two T7 promoter primer membersin an amplification oligomer combination gave consistently good resultsat detecting 1000 copies of SEQ ID NO:91 per reaction. Similar resultswere seen with detection of 1000 copies of SEQ ID NOS:92 & 93, thoughnot every combination produced a detectable product. Further, thesubstitution of a nucleotide residue with an inosine at mismatch sitesresulted in amplification oligomer combinations with equivalent S:N,suggesting that the substitution provided similar amplificationefficiencies. From the above data, SEQ ID NOS:50, 73, 78 were theselected amplification oligomer combination for continued testing.

Example 8: Qualitative TMA/HPA for the Detection of Parvovirus Types 1,2 and 3

The objective of this example was to determine whether an amplificationoligomer combination selected from Example 7 could detect humanparvovirus from infected plasma samples. A further objective was toidentify the end-point of detection using a blinded panel of plasmasamples containing genotypes 1, 2 or 3 of parvovirus. The 2nd WHOInternational Standard (IS) for parvovirus DNA (IS 99/802, NIBSC)) wasused as a positive control. The amplification oligomer combination usedin this example was SEQ ID NOS:50, 73 & 78.

Target material was contained in five separate vials. One of the fivevials was labeled 2nd WHO IS for B19V DNA (99/802) and contained theinternational standard for parvovirus (available from). The remainingfour samples were each labeled #1, #2, #3 or #4, and each containedplasma infected with parvovirus, type 1, type 2, type 3 or containeduninfected plasma as determined by anti-b19 IgG and IgM. A first assaytested for the end-point of detection for the samples from a series often-fold dilutions. Starting from a thawed plasma sample, or, for IS99/802, starting from a lyophilized sample reconstituted to 1 millionIU/ml, a series of five ten-fold dilutions were prepared in order todetermine (a) whether parvovirus DNA can be detected in the sample usingthe amplification oligomer combination, and (b) if detected, thedilution end point of that detection. Results are reported as positive(+) or negative (−) in Table 11. A second assay tested two half-logdilutions either side of the end-point determined in the first assay.Results are reported as positive (+) or negative (−) in Table 12.

Following preparation and dilution of the samples, each sample dilutionwas then mixed with lysing and capturing reagent containing SEQ ID NO:1target capture oligomer comprising a dA30 3′ tail. The mixture wasincubated (60.deg. C, 20 min) to allow the capture oligomer to hybridizeto any parvovirus target DNA in the sample. The mixtures furthercontained homopolymeric oligomers complementary to the 3′-tail portionof the capture oligomer and attached to magnetic particles. Thesehomopolymeric complementary sequences hybridized in a secondhybridization reaction (25.deg. C, 14-20 min) and the hybridizationcomplexes that attached to the magnetic particles were separated fromthe rest of the sample and washed (e.g., twice with 1 ml of a bufferthat maintains the hybridization complexes on the particles) beforeproceeding to amplification. After the samples were treated with thecapture reagent, the magnetic particles with the attached hybridizationcomplexes were incubated in an amplification mixture containing 15 pmolper reaction of each amplification oligomer member in the amplificationoligomer combination SEQ ID NOS:50, 73 & 78, and the appropriate salts,nucleotides and enzymes for a one-hour TMA reaction (substantially asdescribed in detail previously in U.S. Pat. Nos. 5,399,491 and5,554,516). The detection probe of SEQ ID NO:42 labeled between residues9 and 10 with 2-methyl-AE was added (0.1 pmol per reaction) andincubated (60.deg. C, 20 min) with the amplification products to allowhybridization. Chemiluminescent signal was detected (RLU) as describedin detail previously (U.S. Pat. Nos. 5,283,174, 5,656,207, and5,658,737). Results are presented in Tables 11-12. Though a S:N of 10 isuseful, higher S:N are preferred. here, reaction wells resulting in aS:N value of at least 30 were determined to be reactive. (+)=Reactive;(−)=Not Reactive; (NT)=Not Tested.

TABLE 11 First Estimation of End-Point Dilution Stock 10.sup.-110.sup.-2 10.sup.-3 10.sup.-4 10.sup.-5 10.sup.-6 10.sup.-7 IS (99/802)NT + + + − − − NT #1 NT + + + − − − NT #2 NT + + + − + − NT #3 NT + + −− − − NT #4 NT − − − − − − NT

TABLE 12 Second Estimation of End-Point Dilution +/− #1 10.sup.-310.sup.-3.5 10.sup.-4 10.sup.-4.5 10.sup.-5 + + − − − + + + − − + − + −− #2 10.sup.-4 10.sup.-4.5 10.sup.-5 10.sup.-5.5 10.sup.-6 + + − −− + + + − − + − − − − #3 10.sup.-2 10.sup.-2.5 10.sup.-3 10.sup.-3.510.sup.-4 + + + − − + + + − − + + + − − #4 0 10.sup.-0.5 10.sup.-110.sup.-1.5 10.sup.-2 − − − − − − − − − − − − − − − IC (99/802)10.sup.-3 10.sup.-3.5 10.sup.-4 10.sup.-4.5 10.sup.-5 + + + − − + + + +− + + − − −

Parvovirus DNA was detected in each of samples #1, #2 and #3 as well asin the IC positive control sample. No parvovirus was detected in sample#4, indicating that this sample was the negative control. Samples #1, #2and #3 were then sequenced and sequencing confirmed that these samplescontained a parvovirus genotype 1, 2 or 3, respectively. Thus,parvovirus genotypes 1, 2 and 3 were detected from plasma samples.

Example 9: Detection of Parvovirus Types 1, 2 and 3

The object of this example is to test different amplification oligomercombinations for their ability to amplify types 1, 2 and 3 parvovirusDNA. In this example, a first amplification oligomer combinationcomprised SEQ ID NOS:13, 51, 23 and 56. SEQ ID NOS:13 and 23 are a nonT7primer and a T7 promoter primer, respectively, are described in Examples3-6, and have been shown to produce detectible amplicons from samplescontaining human parvovirus. SEQ ID NOS:51 and 56 are a nonT7 primer anda T7 promoter primer, respectively, and are also present in this firstamplification oligomer combination. SEQ ID NO:56 comprises a targetbinding domain (SEQ ID NO:57) and a T7 RNA polymerase promoter sequence(SEQ ID NO:19). A second amplification oligomer combination comprisedSEQ ID NOS:47, 73 & 78. Within this second amplification oligomer designare two T7 promoter primers, SEQ ID NO:73 and SEQ ID NO:78. SEQ ID NO:73comprises a target binding domain (SEQ ID NO:75), an insert tag sequence(SEQ ID NO:94), an inosine residue (n=I) and an RNA polymerase region(SEQ ID NO:19). SEQ ID NO:78 comprises a target binding domain (SEQ IDNO:80), as well as an insert tag sequence (SEQ ID NO:94), two inosineresidues (n=I) and an RNA polymerase region (SEQ ID NO:19). Also withinthe second amplification oligomer combination is a nonT7 primercomprising a target binding domain (SEQ ID NO:48) and a 5′tag sequence(SEQ ID NO:95).

Target material was the same as that used in Example 8; namely, IS99/802, sample #1, sample #2, sample #3 and sample #4. The targetcapture oligomer used with both amplification oligomer combinationconfigurations was SEQ ID NO:53. The detection oligomer used with bothamplification oligomer combination configurations was SEQ ID NO:42.Samples were serially diluted and each dilution was mixed with lysingand capturing reagent containing SEQ ID NO:53, as described above.Captured target were then incubated in amplification mixtures containingthe first or the second amplification oligomer combination, followed bychemiluminescent detection. Results are presented in Tables 13-14

TABLE 13 Amplification Oligomer Combination Performance-10-FoldDilutions SEQ ID NOS: 13, SEQ ID NOS: 51, 23 and 56 47, 73 and 78 S/CoS/Co IS 99/802 10.sup.-2 25.58 32.37 IS 99/802 10.sup.-3 11.04 33.47 IS99/802 10.sup.-4 0.35 0.00 Sample #1 10.sup.-2 26.28 34.32 Sample #210.sup.-2 4.48 34.26 Sample #3 10.sup.-2 1.85 26.14

TABLE 14 Amplification Oligomer Combination Performance-Half-logDilutions SEQ ID NOS: 13, SEQ ID NOS: 51, 23 and 56 47, 73 and 78Average S/Co Average S/Co IS 99/802 10.sup.-3 6.34 31.03 IS 99/80210.sup.-3.5 2.60 18.69 IS 99/802 10.sup.-4 0.24 10.80 IS 99/80210.sup.-4.5 0.28 2.63 IS 99/802 10.sup.-5 0.18 0.04 Sample #1 10.sup.-38.56 29.34 Sample #1 10.sup.-3.5 5.78 9.31 Sample #1 10.sup.-4 0.2811.13 Sample #1 10.sup.-4.5 0.44 0.10 Sample5 #1 10.sup.-5 0.22 0.06Sample #2 10.sup.-3 0.26 10.53 Sample #2 10.sup.-3.5 0.29 14.70 Sample#2 10.sup.-4 0.25 2.20 Sample #2 10.sup.-4.5 0.14 0.05 Sample #210.sup.-5 0.11 0.37 Sample #3 10.sup.-3 1.89 23.60 Sample #3 10.sup.-3.50.73 23.06 Sample #3 10.sup.-4 0.36 17.99 Sample #3 10.sup.-4.5 0.240.26 Sample #3 10.sup.-5 0.38 0.09

In this example, these data showed that the amplification oligomercombination SEQ ID NOS:47, 73 and 78 detected human parvovirus types 1,2 and 3 with a sensitivity to about 100 copies. These data also showthat the SEQ ID NOS:47, 73 and 78 amplification oligomer combinationdetected parvovirus genotype 1 with better sensitivity than did the SEQID NOS:13, 51, 23 and 56 amplification oligomer combination. These dataalso showed that the SEQ ID NOS:47, 73 and 78 amplification oligomercombination detected types 2 and 3 parvovirus, while the SEQ ID NOS:13,51, 23 and 56 amplification oligomer combination did not.

TABLE 15 Exemplary Oligomers, Reference Sequences and Regions SEQ ID NO:Sequence (5′to 3′) 1 gttggctatacctaaagtcatgaatcct TCO. [TBS] only. 2gccagttggctatacctaaagtcatgaatc TCO. [TBS] only. ct 3aatttaatacgactcactatagggagacta T7. [PRO/SEQ ID ggttctgcatgactgctactggaNO:19] + [TBS/SEQ ID NO: 4]. 4 ctaggttctgcatgactgctactggaT7. [TBS] only. 5 aatttaatacgactcactatagggagactg T7. [PRO/SEQ IDcatgactgctactggatgataag NO: 19] + [TBS/SEQ ID NO: 6]. 6ctgcatgactgctactggatgataag T7. [TBS] only. 7aatttaatacgactcactatagggagacta T7. [PRO/SEQ IDggttctgcatgactgctactggatga NO: 19] + [TBS/SEQ ID NO: 8]. 8ctaggttctgcatgactgctactggatga T7. [TBS] only. 9aatttaatacgactcactatagggagagtt T7. [PRO/SEQ ID ctgcatgactgctactggatgaNO: 19] + [TBS/SEQ ID NO: 10]. 10 gttctgcatgactgctactggatgaT7. [TBS] only. 11 aatttaatacgactcactatagggagattc T7. [PRO/SEQ IDtcctctaggttctgcatgactgc NO: 19] + [TBS/SEQ ID NO: 12]. 12ttctcctctaggttctgcatgactgc T7. [TBS] only. 13 cccctagaaaacccatcctctPrimer. [TBS] only. 14 ctctccagacttatatagtcatcattttc Primer. [TBS] only.15 ctctccagacttatatagtcatcat Primer. [TBS] only. 16atcccctagaaaacccatcctct Primer. [TBS] only. 17 gacagttatctgaccacccccatgcProbe. [TBS] only. 18 catggacagttatctgaccacc Probe. [TBS] only. 19aatttaatacgactcactatagggaga Promoter sequence. 20catcactttcccaccatttgccacttt TCO. [TBS] only. 21gcaaatttatcatcactttcccaccatttg TCO. [TBS] only. cc 22aggattcatgactttaggtatagccaac Region. 23 aatttaatacgactcactatagggagaagtT7. [PRO/SEQ ID accgggtagttgtacgctaact NO: 19] + [TBS/SEQ ID NO: 24]. 24agtaccgggtagttgtacgctaact T7. [TBS] only. 25cttatcatccagtaacagtcatgcagaacc TSS corresponding totagaggagaaaatgcagtattatctagtga residues 2333-2414 ofagacttacacaagcctgggcaa SEQ ID NO: 90. 26 gacagttatctgaccacccccatgccttatTSS corresponding to catccagtaacagtcatgcagaacctagagresidues 2308 to 2414 gagaaaatgcagtattatctagtgaagact of SEQ ID NO: 90.tacacaagcctgggcaa 27 gtcatggacagttatctgac Probe. [TBS] only. 28gtattatctagtgaagacttac Probe. [TBS] only. 29aaagtggcaaatggtgggaaagtgatgata Region. aatttgc 30 ctagtgaagacttacacaagcProbe. [TBS] only. 31 gtgaagacttacacaagcctg Probe. [TBS] only. 32gcagtattatctagtgaagac Probe. [TBS] only. 33gcagtattatctagtgaagacttacacaag Region. cctg 34 CAAAGUCAUGGACAGUUAUCUGProbe. [TBS] only. 35 caaagtcatggacagttatctgaccacccc Region. catgc 36ctgtttgacttagttgctcg Probe. [TBS] only. 37 cucuccagacuuauauagucaucauProbe. [TBS] only. 38 gtcatggacagttatctg Region. 39 gtgaagacttacacaagcTSS corresponding to residues 2389-2406 of SEQ ID NO: 90. 40gtattatctagtgaagac Region. 41 catcactttcccaccatttgcc Portion of Captureprobe TBS. 42 GUAUUAUCUAGUGAAGACUUAC Probe. [TBS] only. 43CUAGUGAAGACUUACACAAGC Probe. [TBS] only. 44 GUGAAGACUUACACAAGCCUGProbe. [TBS] only. 45 caaagtcatggacagttatctg Probe. [TBS] only. 46GCAGUAUUAUCUAGUGAAGAC Probe. [TBS] only. 47GTCATATGCGACGATCTCAGGACAGTTATC Primer. [Tag/SEQ ID TGACCACCCCCATGCNO: 95] + [TBS/SEQ ID NO: 48]. 48 GACAGTTATCTGACCACCCCCATGCPrimer. [TBS] only. 49 GTCATATGCGACGATCTCAGGACAGTTATCPrimer. [Tag/SEQ ID TGACCACC NO: 95] + [TBS/SEQ ID NO: 50]. 50GACAGTTATCTGACCACC Primer. [TBS] only. 51 TCTCTGTTTGACTTAGTTGCTCGPrimer. [TBS] only. 52 ggttggctatacctaaagtcatgaatcctt TCO. [TBS/SEQ IDttaaaaaaaaaaaaaaaaaaaaaaaaaaaa NO: 53] + [dT3/dA30]. aa 53ggttggctatacctaaagtcatgaatcct TCO. [TBS] only. 54 gucauggacaguuaucugacProbe. [TBS] only. 55 GenBank Accession No. DQ234772.1 GI: 78217253,entered Nov. 2, 2005. 56 AATTTAATACGACTCACTATAGGGAGACCA T7. [PRO/SEQ IDACATAGTTAGTACCGGGTAGTTG NO: 19] + [TBS/SEQ ID NO: 57]. 57CCAACATAGTTAGTACCGGGTAGTTG T7. [TBS] only. 58AATTTAATACGACTCACTATAGGGAGACCT T7. [PRO/SEQ IDACGATGCATCCAACATAGTTAGTACCGGGT NO: 19] + [Insert/SEQ AID NO: 94] + [TBS/SEQ ID NO: 60]. 59 CCTACGATGCATCCAACATAGTTAGTACCGT7. [Insert/SEQ ID GGTA NO: 94] + [TBS/SEQ ID NO: 60]. 60CCAACATAGTTAGTACCGGGTA T7. [TBS] only. 61 AATTTAATACGACTCACTATAGGGAGACCAT7. [PRO/SEQ ID ACATAGTTAGTACCGGGTA NO: 19] + [TBS/SEQ ID NO: 60]. 62CCAACATAGTTAGTACCGGGTARTTG T7. [TBS] only. 63AATTTAATACGACTCACTATAGGGAGACCT T7. [PRO/SEQ IDACGATGCATCCAACATAGTTAGTACCGGGT NO: 19] + [Insert/SEQ AGTTGID NO: 94] + [TBS/SEQ ID NO: 57] 64 CCTACGATGCATCCAACATAGTTAGTACCGT7. [Insert/SEQ ID GGTAGTTG NO: 94] + [TBS/SEQ ID NO: 57]. 65CCTACGATGCATCCAACATAGTTAGTACCG T7. [Insert/SEQ ID GGTARTTGNO: 94] + [TBS/SEQ ID NO: 62]. 66 AATTTAATACGACTCACTATAGGGAGACCAT7. [PRO/SEQ ID ACATAGTTAGTACCGGGTARTTG NO: 19] + [TBS/SEQ ID NO: 62].67 AATTTAATACGACTCACTATAGGGAGACCT T7. [PRO/SEQ IDACGATGCATCCAACATAGTTAGTACCGGGT NO: 19] + [Insert/SEQ ARTTGID NO: 94] + [TBS/SEQ ID NO: 62]. 68 AATTTAATACGACTCACTATAGGGAGACCTT7. [PRO/SEQ ID ACGATGCATAGTACCGGGTAGTTGTACGCT NO: 19] + [Insert/SEQAACT ID NO: 94] + [TBS/SEQ ID NO: 24]. 69 CCTACGATGCATAGTACCGGGTAGTTGTACT7. [Insert/SEQ ID GCTAACT NO: 94] + [TBS/SEQ ID NO: 24]. 70agtaccgggtaRttgtaYgctaact T7. [TBS] only. 71CCTACGATGCATagtaccgggtaRttgtaY T7. [Insert/SEQ ID gctaactNO: 94] + [TBS/SEQ ID NO: 70]. 72 AATTTAATACGACTCACTATAGGGAGAagtT7. [PRO/SEQ ID accgggtaRttgtaYgctaact NO: 19] + [TBS/SEQ ID NO: 70]. 73AATTTAATACGACTCACTATAGGGAGACCT T7. [PRO/SEQ IDACGATGCATCCAACATAGTTAGTACCGGGT NO:19] + [Insert/SEQ AnTTGID NO: 94] + [TBS/SEQ ID NO: 75]. 74 CCTACGATGCATCCAACATAGTTAGTACCGT7. [Insert/SEQ ID GGTAnTTG NO: 94] + [TBS/SEQ ID NO: 75]. 75CCAACATAGTTAGTACCGGGTAnTTG T7. [TBS] only. 76AATTTAATACGACTCACTATAGGGAGACCA T7. [PRO/SEQ ID ACATAGTTAGTACCGGGTAnTTGNO: 19] + [TBS/SEQ ID NO: 75]. 77GenBank Accession No.: DQ333428.1 GI:84180808,entered Jan. 8, 2006 with non-sequences updates on Dec. 20, 2007. 78AATTTAATACGACTCACTATAGGGAGACCT T7. [PRO/SEQ IDACGATGCATAGTACCGGGTAnTTGTAnGCT NO: 19] + [Insert/SEQ AACTID NO: 94] + [TBS/SEQ ID NO: 80]. 79 CCTACGATGCATAGTACCGGGTAnTTGTAnT7. [Insert/SEQ ID GCTAACT NO: 94] + [TBS/SEQ ID NO: 80]. 80AGTACCGGGTAnTTGTAnGCTAACT T7. [TBS] only. 81AATTTAATACGACTCACTATAGGGAGAAGT T7. [PRO/SEQ ID ACCGGGTAnTTGTAnGCTAACTNO: 19] + [TBS/SEQ ID NO: 80]. 82 AATTTAATACGACTCACTATAGGGAGACCTT7. [PRO/SEQ ID ACGATGCATagtaccgggtaRttgtaYgct NO: 19] + [Insert/SEQaact ID NO: 94] + [TBS/SEQ ID NO: 70]. 83 TACCCGGTACT Region. 84CAAnTACCCGGTACT Portion of T7 TBS. 85 AGTTAGCGTACAACTACCCGGTACTAACTARegion. TGTTGG 86 gcagtattatctagtgaagacttacacaag TSS corresponding tocctgggcaa residues 2376-2414 of SEQ ID NO: 90. 87catggacagttatctgaccacccccatgcc TSS corresponding tottatcatccagtaacagtcatgcagaacct residues 2304-2409 ofagaggagaaaatgcagtattatctagtgaa SEQ ID NO: 90. gacttacacaagcctg 88catggacagttatctgaccacccccatgcc TSS corresponding tottatcatccagtaacagtcatgcagaacct residues 2304-2449 ofagaggagaaaatgcagtattatctagtgaa SEQ ID NO: 90.gacttacacaagcctgggcaagttagcgta caactacccggtactaactatgttgg 89cttatcatccagtaacagtcatgcagaacc TSS corresponding totagaggagaaaatgcagtattatctagtga residues 2333-2438 ofagacttacacaagcctgggcaagttagcgt SEQ ID NO: 90 acaactacccggtact 90GenBank Accession No. DQ225149.1 GI:77994407,entered Oct. 26, 2005, with non-sequence updates on Sep. 12, 2006. 91AGTCATGGACAGTTATCTGACCACCCCCAT Type 1 syntheticGCCTTATCATCCAGTAGCAGTCATGCAGAA construct. CCTAGAGGAGAAAATGCAGTATTATCTAGTGAAGACTTACACAAGCCTGGGCAAGTTAGC GTACAACTACCCGGTACTAACTATGTTGGGCCTGGCAATGAGCTACAAGCTG 92 AGTCATGGACAGTTATCTGACCACCCCCATType 2 synthetic GCCTTATCACCCAGTAGCAGTCATACAGAA construct.CCTAGAGGAGAAAATGCAGTATTATCTAGT GAAGACTTACACAAGCCTGGGCAAGTTAGCATACAACTACCCGGTACTAACTATGTTGGG CCTGGCAATGAGCTACAAGCTG 93AGCCATGGACAGTTATCTGACCACCCCCAT Type 3 syntheticGCCTTATCACCCAGTAACAGTAGTACAGAA construct. CCTAGAGGAGAAAATGCAGTATTATCTAGTGAAGACTTACACAAGCCTGGGCAAGTTAGC ATACAATTACCCGGTACTAACTATGTTGGGCCTGGCAATGAGCTACAAGCTG 94 CCTACGATGCAT Insert sequence 95GTCATATGCGACGATCTCAG Tag sequence 96 catggacagttatctgaccacccccatgcRegion. 97 tacccggtactaactatgttgg Region. 98cttatcatccagtaacagtcatgcagaacc TSS corresponding totagaggagaaaatgcagtattatctagtga residues 2333-2409 of agacttacacaagcctgSEQ ID NO: 90. 99 gcagtattatctagtgaagacttacacaag TSS corresponding tocctgggcaagttagcgtacaactacccggt residues 2376-2438 of act SEQ ID NO: 90.100 gacagttatctgaccacccccatgccttat TSS corresponding tocatccagtaacagtcatgcagaacctagag residues 2308-2438 ofgagaaaatgcagtattatctagtgaagact SEQ ID NO: 90tacacaagcctgggcaagttagcgtacaac tacccggtact Legend: TCO = Target CaptureOligomer. TBS = Target Binding Sequence. TSS = Target Specific Sequence.T7 = promoter based amplification oligomer. Primer = Primeramplification oligomer. Probe = Detection probe oligomer.

The present invention has been described in the context of particularexamples and preferred embodiments. Those skilled in the art willappreciate that other embodiments are encompassed within the inventiondefined by the claims that follow.

We claim:
 1. A detection probe oligomer comprising: (a) a target-bindingsequence that is SEQ ID NO:27, SEQ ID NO:28, SEQ ID NO:32, or SEQ IDNO:36; and (b) a detectable label.
 2. The detection probe oligomer ofclaim 1, wherein the detectable label is a chemiluminescent orfluorescent label.
 3. The detection probe oligomer of claim 1, whereinthe detectable label is a homogeneous detectable label.
 4. The detectionprobe oligomer of claim 3, wherein the homogeneous detectable label is achemiluminescent label.
 5. The detection probe oligomer of claim 4,wherein the chemiluminescent label is an acridinium ester (AE) compound.6. The detection probe oligomer of claim 1, wherein the detection probeoligomer has at least one 2′-methoxy linkage in the nucleic acidbackbone.
 7. A probe reagent comprising: (a) a detection probe oligomercomprising (i) a target-binding sequence that is SEQ ID NO:27, SEQ IDNO:28, SEQ ID NO:32, or SEQ ID NO:36, and (ii) a detectable label; (b)succinate (c) lithium chloride; (d) lithium lauryl sulfate; (e) at leastone anti-coagulant selected from the group consisting of EDTA and EGTA;and (f) ethanol.
 8. The probe reagent of claim 7, wherein the lithiumlauryl sulfate is present in the reagent at a concentration of 2% (w/v).9. The probe reagent of claim 7, wherein the EDTA is present in thereagent at a concentration of 20 mM.
 10. The probe reagent of claim 7,wherein the EGTA is present in the reagent at a concentration of 20 mM.11. The probe reagent of claim 7, wherein the succinate is present inthe reagent at a concentration of 100 mM.
 12. The probe reagent of claim7, wherein the detection probe oligomer has at least one 2′-methoxylinkage in the nucleic acid backbone.
 13. A method for the detection ofan amplified human parvovirus nucleic acid comprising the steps of: (a)providing an amplified human parvovirus nucleic acid comprising a targetspecific sequence that contains SEQ ID NO:88, or comprising a targetspecific sequence amplifiable with a primer consisting of SEQ ID NO:13and a promoter primer consisting of SEQ ID NO:23; (b) hybridizing theamplified human parvovirus nucleic acid with a detection probe oligomer,wherein the detection probe oligomer comprises (i) a target-bindingsequence that is SEQ ID NO:27, SEQ ID NO:28, SEQ ID NO:32, or SEQ IDNO:36, and (ii) a detectable label; and (c) detecting the label of thehybridized detection probe oligomer, thereby detecting the amplifiedhuman parvovirus nucleic acid.
 14. The method of claim 13, wherein thedetectable label is a chemiluminescent or fluorescent label.
 15. Themethod probe oligomer of claim 13, wherein the detectable label is ahomogeneous detectable label.
 16. The method oligomer of claim 15,wherein the homogeneous detectable label is a chemiluminescent label.17. The method oligomer of claim 16, wherein the chemiluminescent labelis an acridinium ester (AE) compound.
 18. The method of claim 13,wherein the detection probe oligomer has at least one 2′-methoxy linkagein the nucleic acid backbone.
 19. The method of claim 13, furthercomprising the step of performing an isothermal amplification reactionon a sample suspected of containing human parvovirus to generate theamplified human parvovirus nucleic acid.
 20. The method of claim 19,wherein the isothermal amplification reaction is atranscription-mediated amplification reaction.